Babs1201 s1 2018 Manual RLB

FACULTY OF SCIENCE
SCHOOL OF BIOTECHNOLOGY AND BIOMOLECULAR SCIENCES
BABS1201
MOLECULES, CELLS & GENES
Session 1
2018
Student Name:
Tutor:
1
CONTENTS
Welcome 2
Quick Answers to BABS1201 FAQs 3
BABS1201 Weekly Class and Assessment Schedule 5
Course Identity 6
Course Resources 7
Course Assessment Schedule and Summary 8
Course Outline 10
Course Structure 11
Graduate Attributes 12
Lecture Program 13
Administrative Matters 17
Special Consideration and Further Assessment 18
Academic Honesty and Plagiarism 19
Course Assessment – Detailed instructions 20
- Online laboratory safety quiz 20
- Mid-session tests I and II 21
- Science communication project 22
- Scientific literature essay 30
- Mastering biology and final exam 32
Introduction to Laboratory Safety 33
Practical 1: Cell Structure I - Looking at cells using the light microscope 49
Practical 2: Cell Structure II - Comparing cells using the light microscope 56
Practical 3: Cell Function I - Osmosis and diffusion 70
Practical 4: Cell Function II - Photosynthesis and respiration 85
Practical 5: Genes I – Mitosis and meiosis 101
Practical 6: Genes II – Genetic inheritance 117
2
Welcome to BABS1201 Molecules, Cells and Genes
This course aims to introduce you to the basic concepts of modern biology, and to
develop your skills in scientific analysis and critical thinking – skills that will be useful
in science and other careers.
The course consists of three interconnected learning components: a lecture series, a

laboratory program, and online activities. These classes sequentially address cell
structure, cell function and genes. The laboratory program comprises both practical
and theoretical components. You will also be directed to electronic resources that
revise and reinforce the concepts covered in the course.
To be ready for your first classes, ensure that you have purchased or printed a copy
of the Course Manual (available from the UNSW Bookshop or the course Moodle
site). In preparation for your lectures, you can download the notes from Moodle and
can read relevant material from the course textbook (available from the UNSW
Bookshop, as an ebook or from the library).
Prior to your laboratory classes, you need to purchase a laboratory coat and safety
glasses (available at various stores on campus) and, before Practical 1, complete an
online Health and Safety quiz. You must come to your timetabled lab class with a
copy of the Course Manual, appropriate stationery and wearing closed shoes. As
electronic resources will be used in class, you as encouraged to bring a laptop, tablet
or similar device. If you do not have access to one, let your demonstrator know and
we can arrange one for you.
To ensure you are organised for the year, look ahead in this outline for the due dates
of assignments and enter them into your diary. Details of the assignments are
included in this Course Manual and further information will be posted on Moodle as
the due dates approach. It is your responsibility to ensure you can access the
Mastering Biology resources via Moodle well before your first quiz.
If you have a question that has not been addresed in the resources provided, please
post on the course Moodle forum. If your question is sensitive or of a personal nature,
email BABS1201@unsw.edu.au, with is directed to both of us and the course
administrator. Our laboratory classes are run relatively informally, so you are
welcome to ask questions and discuss the material with your demonstrators in class
as needed.
We hope your study of biology this session will be interesting, enjoyable and
rewarding.
We look forward to teaching you.
Rebecca and John
Course Convenors
3
QUICK ANSWERS
QUICK ANSWERS TO
TO BABS1201
BABS1201 FAQS
FAQS
GENERAL
• I have a question about the course. Where do I find the answer?
1. Look in this manual. Use the table of contents on page 1 to help you.
2. Check the BABS1201 Moodle site: https://moodle.telt.unsw.edu.au/login/index.php
3. Post your question to the forums in the BABS1201 Moodle site.
4. Email your question to BABS1201@unsw.edu.au (this option is especially useful when your
question is of a personal or sensitive nature). ALWAYS include your full name and student
number in ALL email correspondence, and send from your UNSW email account
5. Take the time to clearly word your query.
• How do I find answers to questions about specific lecture material?

1. Read through the corresponding lecture notes whilst listening to the lecture audio recording
(lecture notes and recordings can be accessed through the BABS1201 Moodle site). The
lecturer may have answered your question during the lecture.
2. Refer to the corresponding reference(s) provided by the lecturer. If references are not provided
or are not related to your question, use the index of a biology text book (even if it is not the
recommended text for the course) to search for information on the topic of interest. There are
also copies of the recommended text in the library.
3. Use the Mastering Biology revision materials available via Moodle.
4. Post your question on a discussion forum in the BABS1201 Moodle site.
5. Email your question to BABS1201@unsw.edu.au, including your full name and student number,
as well as the full details of the exact lecture to which your question refers.
• How do I contact my demonstrator? Can I email them?

No, you cannot directly contact your demonstrator as they are only employed beyond their face-to-
face hours. You can instead post your question to the Moodle forums for your convenor or the
course administrator to answer. In this way, all students will have a chance to see the answer. If
the matter is not on the content of the course eg. it relates to your attendance, you can email your
question (clearly indicating your laboratory class and demonstrator name) to
BABS1201@unsw.edu.au, and, if necessary, it will be forwarded to your demonstrator. Otherwise,
your question can be addressed directly by your demonstrator during the next laboratory class.
• Will I have access to past BABS1201 exam papers?

No, past BABS1201 exams are not available to students. Sample questions are provided
throughout the course and the Mastering Biolgy activities are particularly useful for exam
preparation.
ABSENCES AND ASSESSMENTS
• I missed a lab class. What should I do?

Attendance at all lab classes is compulsory. If you miss a lab class due to illness or some other
unavoidable circumstance that can be explained using professional documentation (e.g. a medical
certificate), you should provide your demonstrator with this documentation the following week.
4
• I missed the mid-session exam. What should I do?

If you miss the mid-session exam due to illness or some other unavoidable circumstance that can
be explained using professional documentation (e.g. a medical certificate), you should apply for
Special Consideration online (see page 18 for instructions). You will be notified of the outcome of
your application before the end of session through myUNSW and/or your UNSW email account.
• I could not submit my assessment on time. What should I do?

If you cannot submit your essay or practical report by the due date due to illness or an unavoidable
circumstance that can be explained using professional documentation (e.g. a medical certificate),
you should apply for Special Consideration online (see page 18 for instructions) and submit the
assessment item as soon as possible. You will be notified of the outcome of your application
before the end of session through myUNSW and/or your UNSW email account. If you do not
submit an assessment item by the submission deadline and you do not have a valid excuse, the
appropriate late penalties will be applied to your final mark for that assessment item.
• I missed (or was sick during) the final exam. What should I do?
If you miss the final exam due to illness or some other unavoidable circumstance that can be
explained using professional documentation (e.g. a medical certificate), you should apply for
Special Consideration online (see page 18 for instructions). If you were sick DURING the exam,
you should obtain a medical certificate on the day of the exam and apply for Special
Consideration online (see page 18 for instructions). You will be notified of the outcome of your
application and details of the supplementary examination (if applicable) through your UNSW e-mail
account. See page 18 for details of the supplementary exam.
Please note that if you are offered a supplementary exam, you will only be given one opportunity to
attend this, unless there are exceptional circumstances.
5
BABS1201 Weekly Class and Assessment Schedule – S1, 2018
LECTURE A LECTURE B
Week Week Monday 9-10 am John Clancy Friday 9-10 am John Clancy Laboratory Laboratory
Assessments
No. Commencing Auditorium OR Tuesday 9-10 am Auditorium OR Friday 5-6 pm (even weeks) (odd weeks)
Ritchie Theatre Mathews Theatre A
Introduction to Introduction to Online lab safety

1 26-Feb 1. Course introduction – RLB/JW 2. Cells I - RLB
laboratory safety* laboratory safety* quiz
Prac 1 Cell structure Scientific literature
2 5-Mar 3. Cells II - RLB 4. Macromolecules I (CHO & fats) - RLB -
I module online**
Scientific literature Prac 1 Cell structure
3 12-Mar 5. Macromolecules II (Proteins) - RLB 6. Macromolecules III (DNA) - LLM -
module online** I
Mastering biology
Prac 2 Cell Structure
4 19-Mar 7. Cell integrity VS 8. Nutrient and ion transport - VS - quiz 1
II
Prac 2 Cell Structure
5 26-Mar MID-SESSION TEST I PUBLIC HOLIDAY Mid-session test 1
II
- 2-Apr MID-SESSION BREAK
6 9-Apr 9. Metabolism I – JW 10. Metabolism II - JW Prac 3 Cell function I Essay due Prac 3
7 16-Apr 11. Photosynthesis - RLB 12. DNA Replication - LLM Prac 3 Cell function I
Pitch in Prac 4
Prac 4 Cell function
8 23-Apr 13. Cell division and reproduction - LLM 14. Gene expression I - LLM Mastering biology
II
Quiz 2
Prac 4 Cell function Mastering biology
9 30-Apr 15. Gene expression II - LLM 16. Polymerase Chain Reaction - LLM
II Quiz 3
Mastering biology
10 7-May MID-SESSION TEST II 17. Mutation - AMG Prac 5 Genes I -
Quiz 4
11 14-May 18. Mendel’s Laws of Heredity - PW 19. Mechanisms of Inheritance - PW - Prac 5 Genes I Mid-Session Test 2
Presentations,
12 21-May 20. Population Genetics - PW 21. Tips and tricks – JW / RLB Prac 6 Genes II - portfolios and
reflections Prac 6
Mastering biology
13 28-May No lecture No lecture - Prac 6 Genes II
Quiz 5
JW:John Wilson, RLB: Rebecca LeBard, LLM: Louise Lutze-Mann, VS: Vladimir Sytnyk, PW: Paul Waters
*Introduction to laboratory safety can be found on page 33 of your Course Manual and is to be completed outside of class hours.
** The ‘Scientific Literature’ module is found on Moodle and is to be completed outside of class hours.
6
Course Identity
Course Code BABS1201
Course Name Molecules, Cells & Genes
Academic Unit School of Biotechnology and Biomolecular Sciences
Level of Course First Year Undergraduate

Units of Credit 6
Assumed Knowledge,
Nil
Prerequisites or Co-requisites
Hours per Week 5
Number of Weeks 13 weeks
Dr Rebecca LeBard
Room 103, Level 1, Biological Sciences Building (eastern end)
Å (02) 9385 2026; Meetings by appointment only.
Email: r.lebard@unsw.edu.au
Course Convenors
John Wilson
Room G27 (inside the BSB Office), Biological Sciences Building
Å (02) 9385 8156; Meetings by appointment only.
Email: j.e.wilson@unsw.edu.au
Sally Crane
BABS1201 Course Administrator
Administrative Support E-mail: BABS1201@unsw.edu.au

(enrolment queries, academic BABS/SOMS/BEES (BSB) Student office
advise etc)
Room G27, Ground floor, Biological Sciences Building
Å (02) 9385 8047; Opening Hours: 9:00am – 4:30pm, Mon-Fri.
Email: BABStudent@unsw.edu.au
7
Course Resources
Recommended Reece, Jane B., Noel Meyers, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman,
Peter V. Minorsky, Robert B. Jackson, Bernard Cooke, and Neil A. Campbell. 2015.
Textbook Campbell biology.
The textbook is available for purchase at the UNSW bookshop in print form and in
electronic format via http://www.pearson.com.au/9781488619878.
This textbook complements the Mastering biology learning resources available to

you throughout the course accessable from the course Moodle site.
Multiple hard copies are available from the UNSW library and they have an
electronic version. Search the library catalogue for “Campbell Biology Australian
and New Zealand Edition.”
BABS1201 uses Moodle as an on-line course management software. This website

Course contains background information, links to resources, lecture notes, and discussion
forums. Once you are enrolled in BABS1201, you can access the Moodle site at:
Web Site
https://moodle.telt.unsw.edu.au/login/index.php
Your username is your student number preceded by a lower-case ‘z’
e.g. z1234567.
Your password is your zpass.
Course A course manual is required and may be purchased from the UNSW Bookshop or
Manual downloaded from the BABS1201 Moodle site.
Please Note: If you choose to print your own copy, make sure that you bind it or file
it in a folder and bring the COMPLETE manual to all lab classes.
For all practical classes students are required to bring:
Practical • The complete BABS1201 Molecules, Cells & Genes Course Manual. Read the
Class instructions in advance for each practical.
Requirements • A laboratory coat and closed shoes. This is required by Health and Safety (HS)
regulations, and you will not be permitted to participate in practicals if you are
inappropriately clothed. If you have long hair, you must also wear it tied back
during practical classes. Laboratory coats can be purchased from various stores
on campus.
• Material for recording your observations and findings as appropriate for each
class. These items include: a pen, an HB pencil, eraser, ruler and lined paper for
written observations and plain paper for drawings.
8
Course Assessment Schedule & Summary

Assessment Brief Description Due Date Weight
A. Online This online laboratory safety quiz is accessable through the

Before
Laboratory BABS1201 Moodle site. It is COMPULSORY to complete this Practical 1
N/A
SafetyQuiz quiz with a mark of 100% BEFORE your first practical class.
TEST 1 Duration: 40 minutes. Format: multiple choice
questions. Content: all theory and practical material from Weeks Week 5
B. Session Tests 1-4 (inclusive). Venue: online Time: your enrolled lecture time
I and II
20%
TEST 2 Duration: 40 minutes. Format: multiple choice
questions. Content: all theory and practical material from Weeks Week 10
6-9 (inclusive). Venue: online Time: your enrolled lecture time
ESSAY. You must prepare and submit your INDIVIDUAL essay
in class (hard copy) and online via the Turnitin plagiarism Practical 3
10%
checking software in Moodle. Check Moodle announcements Week 6/7
regularly for any changes.
PITCH. TEAM presentation of ideas to your laboratory group for
peer feedback on the design, biological content and feasibility of Practical 4
5%
their project whilst providing similar feedback to other project Week 8/9
teams in the class
PRESENTATION. Utilise the peer feedback received in the pitch Practical 6
C. Science to finalise your TEAM presentation on your advanced biology Week 10%
Communication topic for submission and showcasing at the end of session 12/13
Project
PORTFOLIO. TEAM submission documenting the proceedings
Practical 6
of all team meetings, including an inventory of ideas, team
Week 5%
member roles, major decisions, and other notes on the
12/13
presentation design and execution.
REFLECTIVE SUMMARY. An INDIVIDUAL describes your
personal learning from both positive and negative experience
Practical 6
throughout the duration of the Project, including a peer
Week 5%
evaluation of team member contributions to all components of
12/13
the project, and how any problems could have been better
managed by the team.
Online Mastering biology tasks designed to provide you with
formative feedback on how you are progressing in the course.
Each task is a short quiz (15-30 minutes) worth 1% of your final 11:59pm
D.Mastering assessment for the course. Friday
biology Weeks 4, 8,
5%
It is highly recommended that you at least complete the online 9, 10 and 13
activities detailed in the manual in the weeks you do not have a
laboratory class in preparation for these quizzes.
Duration: 2 hours. Format: the front page of the exam paper, June
detailing the format (including the number and type of questions) (Date to be
H. Final Theory
Exam
will be available uploaded to Moodle after submission to the advised by 40%
exams branch. Content: all theory and practical material from exams
Weeks 1-13 of session. branch)
9
Mastering Biology Assessment Schedule and Summary

DATE
MEDIAN AVAILABLE
TIME ONLINE DATE DUE
QUIZ 1: PROKARYOTIC VERSUS EUKARYOTIC Week 3 Week 4
CELL STRUCTURE 12 March 23 March
Activity: Prokaryotic Cell Structure and Function 5 min
Activity: Review: Animal Cell Structure and Function 9 min
Total time 14 min
Week 7 Week 8
QUIZ 2: OSMOSIS AND DIFFUSION
16 April 27 April
Activity: Selective Permeability of Membranes 2 min
Activity: Diffusion 1 min
Activity: Diffusion and Osmosis 6 min
Activity: Facilitated Diffusion 1 min
Activity: Osmosis and Water Balance in Cells 4 min
Activity: Active Transport 2 min
Total time 15 min
Week 8 Week 9
QUIZ 3: PHOTOSYNTHESIS
23 April 4 May
Activity: Overview of Photosynthesis 3 min
Activity: The Sites of Photosynthesis 1 min
Tutorial: Energy Flow in Plants - Concept Map 3 min
Activity: The Light Reactions 4 min
Activity: Photosynthesis 5 min
Activity: The Calvin Cycle 3 min
Total time 19 min
Week 9 Week 10
QUIZ 4: MITOSIS AND MEIOSIS
30 April 11 May
Activity: Mitosis and Cytokinesis Animation 8 min
Activity: The Cell Cycle 3 min
Activity: Meiosis Animation 10 min
Total time 21 min
Week 12 Week 13
QUIZ 5: DNA STRUCTURE AND REPLICATION
21 May 1 June
Activity: DNA and RNA Structure 8 min
Activity: DNA Replication: A Closer Look 4 min
Tutorial: DNA Replication 2 min
Activity: DNA Replication: A Review 4 min
Activity: DNA Replication: An Overview 3 min
Activity: DNA Synthesis 4 min
Total time 25 min
EACH QUIZ IS WORTH 1% OF YOUR FINAL ASSESSMENT (5% TOTAL).
Quizzes are not timed, but each must be completed by the due date.
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Course Outline
The course, Molecules, Cells and Genes encompasses four major themes. These themes are not
presented in turn, but rather will be presented in an integrated fashion.
This theme introduces the skills of scientific thinking, including how to decide what is true
Theme 1: or plausible, and how scientists communicate. It also exposes you to cutting edge
Thinking research being conducted at UNSW.
like a
Lectures and practical classes on this theme are interspersed through the session,
scientist
enabling you:
• To comprehend that science is a never-ending exploration, and that knowledge is
provisional.
• To identify the principal characteristics of scientific evidence.
• To understand how scientists approach the investigation of a topic.
• To communicate the principles of scientific findings to other scientists.
This theme describes the principal types of living cells, the key components of cell
Theme 2: structure, their functions, and how they relate to each other.
Cell biology
Lectures and practical classes on this theme should enable you:
and cell
architecture • To understand the evolutionary origins of life, and of the diversity of life.
• To identify the different types of living cells, and the main similarities and
differences between them.
• To explain how different cell types are identified.
• To describe important cell structures and relate these to function.
• To compare and contrast cell structures in eukaryotes and bacteria.
This theme outlines the key concepts of metabolism, the consumption and generation of
Theme 3: energy by living cells.
Metabolism
• To describe the essential differences between proteins, carbohydrates and lipids.
• To describe the processes by which these molecules enter cells.
• To comprehend the processes of generating energy for cellular function.
• To compare and contrast energy generation in animals and plants.
This theme introduces the key concepts of modern genetics, including what genes are,
Theme 4: how they are regulated, how genetic information is transmitted and how modern molecular
Genetics biology can use genetics to understand biology.
• To describe the essential structures of genetic material (nucleic acids, genes,
chromosomes).
• To explain the processes by which cells divide.
• To describe the principal steps in the control of gene expression and the
production of functional proteins.
• To relate these structures and processes to the inheritance of genetic
characteristics.
• To explain the uses of recombinant DNA technology in at least one situation
relating to investigation of gene function.
11
Course Structure
Laboratory based experimentation is an important part of modern biology, and this course
gives you the opportunity to conduct laboratory explorations and to acquire basic skills.
Practical
classes The practical component of this course is designed as an exploration of cell structure and
function, and of the genetic material of those cells. It is divided into three sequences of
practicals that are linked to the lecture series:
o Introduction to laboratory safety
o Exploring cell structure (Practicals 1-2)
o Exploring cell function (Practicals 3-4)
o Exploring genes (Practicals 5-6)
There are aims for each individual practical class, and overall goals for each section.
Each practical class is assessable.
LABORATORY PREPARATION: PRIOR to each class, you are expected to complete
a pre-lab quiz in Moodle.
Your attendance at EVERY laboratory class is COMPULSORY, including the introductory
session on laboratory safety and procedures in Week 1. Should you be unable to attend
your practical class for any reason, you will not be able to do “make-up” labs. For
unavoidable absences from practical classes, you must provide your demonstrator with a
medical certificate or other professional documentation that supports the reason for your
absence. See FAQ on page 3 and Expectations of Students on page 17 for details on
absences from classes.
Lectures emphasise certain principles covered in the text, provide an overview, and
connect the individual components of the course. The lectures also serve to update and
Lectures extend text coverage, using examples from current research. All of the lecturers in
Molecules, Cells and Genes are active in research and have well-established reputations
in the fields in which they teach. At UNSW, the people who teach you biology have made
significant contributions to your area of study.
Unlike high school, we do not take roll at lectures, and there is no compulsion to attend.
There are often ideas or concepts covered in lectures that may not necessarily be dealt
with in your text. Lectures also serve to highlight areas that we believe you should focus
on in the textbook.
We are aware that the students in this course have widely varying backgrounds in
biology, so we are concerned that all students are being appropriately catered for. If you
feel that a lecture is dealing with something that is already familiar to you, you may use it
as an opportunity for revision, or choose not to attend in person.
If you choose to attend, please be quiet when the lecturer is speaking. Chatting makes it
difficult for your fellow students to listen, and for the person giving the lecture. Remember
that it is a real person up there, not a TV screen, and that we can hear you as well as you
can hear us! Repeated disruption of lectures by talking, or through other inappropriate
behaviour, constitutes academic misconduct. Lecturers may also ask a disruptive student
to leave the lecture theatre.
Please note: Mobile phones are to be switched to silent during lectures and practicals.
Lecture notes and recordings are accessible via the BABS1201 Moodle site.
Please be aware that whilst the lecture notes are comprehensive, they are no substitute
for taking your own additional notes based on the lectures and textbook material.
12
UNSW Science Graduate Attributes Developed in this Course

0 = no focus
Science Graduate 1 = minimal
Activities / Assessment
Attributes 2 = minor
3 = major
Research, inquiry and
Guided laboratory practicals; independent and collaborative
analytical thinking 3
lab research; and independent research.
abilities
Capability and
motivation for Small group discussions; essay and project presentation;
3
intellectual Mastering biology online resources.
development
Science communication topics may address some of the
Ethical, social and
ethical and social issues of biology, and the “how to think
professional 2
like a scientist” theme throughout the course addresses
understanding
professional understanding.
Development of scientific writing skills through introduction

Communication 3
to scientific literature (essay); and the project.
Teamwork,
Team independent research project; facilitation of group
collaborative and 3
discussions in class and on Moodle.
management skills
Introduction to finding reviews and primary scientific
Information literacy 3 literature (essay), team project.
Lectures are used to introduce the concepts of fundamental cell biology and
laboratory sessions are used to both complement the lecture material and
provide practise in standard biological techniques used in research.
Laboratories are used to encourage teamwork. Discussion groups and
electronic resources referrred to within scheduled laboratory classes are
additionally designed to further reinforce the concepts presented in lectures
and practised in the laboratory, and support students in their assigned
projects.
The laboratory program forms an essential element of the students’

scientific training. The laboratory program, as integrated with the other
Teaching strategies components of the course, have been designed in accordance with the
UNSW Guidelines on Learning that Inform Teaching
(www.guidelinesonlearning.unsw.edu.au) to:
o Teach students the process of scientific inquiry through progressive

cycles of critical analysis of their research and their own thinking;
o Facilitate multidisciplinary thinking to reflect current research and
professional practice in the sciences;
o Reinforce deep learning and promote collaborative inquiry;
o Integrate students’ disciplinary understanding and research practice
with the development of their communication skills, teamwork, and
information literacy skills.
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Lecture Program
Please note that the lecture topics and learning outcomes listed below are a guide only.
Individual lecturers may provide you with updated topics and learning outcomes.
Lecture topics
What is BABS1201? • Course introduction.
• Use of course resources: lectures, Moodle, and practicals.
• Assessments.
• How to study and excel in your assessments.
• Plagiarism.
Lecture topics
Cells I • What is life?
• Bacteria, archaea and eukaryotes.
• Principal differences between bacteria and eukaryotic cells.
• Evolutionary relationships between cell types.
Learning outcomes
• To understand the characteristics of life.
• To be able to identify the fundamental differences between bacteria
and eukaryotic cells.
• To describe the concept of endosymbiosis.
•
Lecture topics
Cells II • Eukaryote organelle structure and function.
• Bacterial cell structure.
• The cytoskeleton.
Learning outcomes
• To identify characteristic structures of eukaryotic and bacterial cells
and to describe their basic functions.
• To describe the endomembrane system.
• To list the main components of the cytoskeleton and briefly
describe their roles in the cell.
Lecture topics
Macromolecules I • The four main organic components of cells – nucleic acids,
proteins, lipids, carbohydrates.
• Identification of important similarities & differences in
macromolecular structure.
• Introductory concepts of breakdown and synthesis.
• Functions of macromolecules – structural, food storage, enzymes.
Learning outcomes
• To identify characteristic structures of protein, carbohydrate and
lipid molecules.
• To describe the principal elements of their formation from and
breakdown to their molecular subunits.
To identify the importance of these molecules in cell structure and in
nutrition.
Lecture topics
Macromolecules III • What is the genetic information?
(DNA) • An introduction to nucleic acid structure.
• Bases as code.
Learning outcomes
• Describe the basic structure of nucleic acids.
• Explain how genetic information is encoded in nucleic acids.
• Identify the differences between DNA & RNA.
14
Lecture topics
Cell Integrity • Membrane structure.
• The fluid mosaic model.
• The roles of lipids and proteins in maintaining cell integrity.
• Membrane permeability, diffusion and osmosis.
Learning outcomes
• To comprehend the structure of the cell membranes and their
function in maintaining cell integrity.
• To describe the different components of the cell menbrane that play
an important role in maintaining cell integrity.
• To explain the non-selective diffusion of some small molecules
across cell membranes and osmosis.
Lecture topics
Cellular transport • Transporter proteins.
• Passive and active transport.
• Ion transport and membrane potential.
• Vesicular transport.
Learning outcomes
• To explain the mechanisms by which small molecules may be
selectively transported into and out of cells.
• To comprehend the concept of a membrane potential arising from
ionic imbalances across cell membranes.
• To describe the different types of endocytosis.
Lecture topics
Metabolism I: • Catabolism and anabolism.
Metabolic concepts • The role of ATP in "energy" metabolism.
• Nutritional and metabolic diversity.
• Respiration and fermentation.
• Metabolic control.
Learning outcomes
• Explain the differences between anabolism and catabolism.
• Describe the process of cells breaking down molecules to release
chemical energy, render them harmless or allow for recycling.
• Explain the basic model for enzyme catalysis.
• Describe the structure and function of ATP.
• Explain the four main nutritional modes utilised by organisms.
• To comprehend the importance of oxygen and respiration in higher
animals and plants.
• Explain the concept of metabolic control via feedback inhibition.
•
Lecture topics
Metabolism II: • Overview of the catabolism of carbohydrate, fat and protein.
Extracting energy • Overview of glycolysis, the TCA cycle and the respiratory chain.
from food • Chemiosmosis - the formation of ATP by oxidative phosphorylation.
• ATP yields from glucose catabolism.
Learning outcomes
• Describe the convergent catabolism of different macromolecules.
• Describe the central features of glycolysis, the TCA cycle and
oxidative phosphorylation.
• To comprehend the basic principles of chemiosmosis - the
generation of a proton gradient by, for example, the respiratory
chain and the utilisation of the gradient by ATP synthase.
• To explain the advantages of respiration over fermentation with
respect to energy yields.
15
Photosynthesis: Lecture topics
Synthesising food • Overview of photosynthesis.
from energy • Light harvesting.
• The light reactions of photosynthesis.
• The Calvin cycle.
Learning outcomes
• To explain the functions of the different stages in photosynthesis -
light harvesting, the conversion of light energy into chemical energy
and carbon dioxide fixation.
• To explain the overall organisation of the light reactions in
photosystems I and II.
• To outline the fixation of carbon dioxide and synthesis of glucose in
the Calvin cycle.
• To compare and contrast the generation of energy from
photosynthesis and oxidation.
Lecture topics
DNA replication • Mechanisms of DNA synthesis in bacteria and eukaryotes.
Learning outcomes
• Explain the semi-conservative model of DNA replication.
• Describe the basic steps involved in the process of DNA replication.
• Describe the function of the major enzymes involved in DNA
replication.
Lecture topics
Cell division and • Nature of genes and chromosomes.
reproduction • Cell division: mitosis and meiosis.
Learning outcomes
• To explain the difference between a gene and a chromosome.
• To describe the processes of mitosis and meiosis, the differences
between them and their purpose.
Lecture topics
Gene expression I: • DNAàRNAàprotein.
Transcription • The genetic code.
• Transcription: The synthesis of RNA from a DNA template.
• Differences in gene expression between bacteria & eukaryotes.
Learning outcomes
• Describe the genetic code.
• Explain how the instructions contained within DNA are transcribed
into RNA.
• Define the three stages of transcription.
• State the main differences in gene expression between bacteria
and eukaryotes.
Lecture topics
Gene expression II: • Overview: the translation of mRNA into amino acids.
Translation • Transfer RNA and its role in translation.
• The ribosome as the protein synthesis factory.
• The three stages of translation.
• Control of gene expression.
Learning outcomes
• Explain the processes of transcription and translation and relate
them to cell function and the role of ribosomes.
• Describe the basic structure and function of tRNA.
• Describe the three main stages of translation.
• Explain the main differences between control of gene expression in
bacteria and eukaryotes.
16
Lecture topics
The polymerase • Polymerase chain reaction (PCR).
chain reaction
Learning outcomes
• To describe the PCR technique and the basic steps involved.
• To list several applications of the PCR.
Lecture topics
Mutation • Errors in reproduction.
• Environmental influences (radiation, chemicals, viruses).
• “Beneficial mutations” and natural selection.
• Loss of function or changed function.
• Gene duplication.
• Relationship to selected disease.
• Mutations in the immune system.
Learning outcomes
• To explain at mechanisms by which mutations can arise.
• Relate the occurrence of mutations to the outcomes for cells and
whole organisms.
• To appreciate the importance of the rate of mutation for the
evolution of species.
Lecture topics
Mendel’s laws of • Mendel’s laws.
heredity • Essential concepts in genetics: allele vs. locus, genotype vs.
phenotype, homozygosity vs. heterozygosity, recessive vs.
dominant
Learning outcomes
• To describe Mendel’s laws.
• To explain the basis of inherited characteristics.
• To explain why genotype does not always equal phenotype.
Lecture topics
Mechanisms of • Modes of inheritance (single-locus, Mendelian traits).
inheritance • Inheritance of complex traits.
• Vertical inheritance vs. horizontal gene transfer.
Learning outcomes
• To understand the varied modes of inheritance in different
organisms.
Lecture topics
Population genetics • Hardy-Weinberg law.
• Evolutionary forces that change allele and genotype proportions.
Learning outcomes
• To explain the evolutionary forces that influence population
genetics using the Hardy-Weinberg model.
• Overview of BABS1201.
Course review
• Exam structure and tips.
• Student questions.
17
Administrative Matters
A pass in BABS1201 is conditional upon a satisfactory performance in both
Expectations the assessment and practical programs. We expect that you will have:
of Students
o Attempted/submitted all assessment items.
o Attended all of the practical classes (an attendance record is kept).
o Kept an accurate and up-to-date laboratory manual, including the
recording of all data and completion of calculations and questions.
PLEASE NOTE that if students attend less than 80% of their possible
classes they may be refused final assessment. Your attendance at
classes will be monitored. Holidays (local or international) are NOT
considered a valid reason for student absences from classes and
assessments. For more details on UNSW class attendance policies, please
refer to: https://student.unsw.edu.au/attendance
Requirements vary with each assigned task. All information regarding
Assignment
submissions is explained in this manual, by your practical class
Submissions
demonstrator and online via Moodle announcements.
Those students who have a disability that requires some adjustment in their
Equity and Diversity teaching or learning environment are encouraged to discuss their study
needs with the course convenor prior to, or at the commencement of, their
course, or with the Equity Officer (Disability) in the Equity and Diversity Unit
(93854734 or http://www.studentequity.unsw.edu.au/).
Issues may include access to materials, signers or note-takers, the
provision of services and additional exam and assessment arrangements.
Early notification is essential to enable any necessary adjustments.
Information on designing courses and course outlines that take into account
the needs of students with disabilities can be found on the above website.
BABS Marc Wilkins
Student Complaint
School Contact m.wilkins@unsw.edu.au
Procedure
Tel: 9385 3633
Science Gavin Edwards
Faculty Contact Associate Dean (Undergraduate programs)
g.edwards@unsw.edu.au
Tel: 9385 7111
University Contact Student Conduct and Appeals Officer (SCAO)
within the Office of the Pro-Vice-Chancellor (Students) and
Registrar
Tel: 9385 8515
studentcomplaints@unsw.edu.au
18
Special Consideration and Further Assessment

Students who believe that their performance, either during the session or in the
Explanation end of session exams, may have been affected by illness or other circumstances
may apply for special consideration. For BABS1201, applications can be made for
in-session assessments tasks and the final examination.
Students must make a formal application for Special Consideration for the
course/s affected as soon as practicable after the problem occurs and within
three working days of the assessment to which it refers.
Students should consult the “Special Consideration” section of Moodle for specific
instructions related to each BABS course they are studying. Further general
information on special consideration can also be found at
https://student.unsw.edu.au/special-consideration.
Applications must be made via Online Services in myUNSW. You must obtain
How to apply and attach Third Party documentation before submitting the application.
for special Failure to do so will result in the application being rejected. Log into myUNSW and
consideration go to My Student Profile tab > My Student Services channel > Online
Services > Special Consideration. After applying online, students must also
verify their supporting documentation by submitting to UNSW Student Central:
• Originals or certified copies of your supporting documentation, and

• A completed Professional Authority form (pdf - download here).
https://my.unsw.edu.au/student/academiclife/ProfessionalAuthority.pdf
The supporting documentation must be submitted to Student Central for

verification within three working days of the assessment or the period
covered by the supporting documentation. Applications which are not
verified will be rejected.
Further details are also available:

https://my.unsw.edu.au/student/academiclife/ProfessionalAuthority.pdf
Students will be contacted via the online special consideration system as to the
outcome of their application. Students will be notified via their official university
email once an outcome has been recorded.
The University does not give deferred examinations. However, further assessment
Supplementary exams may be given to those students who were absent from the final exams
examinations through illness or misadventure. Special Consideration applications for final
examinations will only be considered after the final examination period when lists
of students sitting supplementary exams/tests for each course are determined at
School Assessment Review Group Meetings. Students will be notified via the
online special consideration system as to the outcome of their application.
It is the responsibility of all students to regularly consult their official

student email accounts and myUNSW in order to ascertain whether or not
they have been granted further assessment.
In Session 1, the BABS1201 Supplementary Examination Period will be:
Saturday 14 July – Saturday 21 July
Further assessment exams will be offered on ONE day in this period only and
failure to sit for the appropriate exam may result in an overall failure for the
course. Further assessment will NOT be offered on any alternative dates.
19
Academic Honesty and Plagiarism
Plagiarism is the presentation of the thoughts or work of another as one’s own.
Examples include:
• Direct duplication of the thoughts or work of another, including by copying work, or knowingly
permitting it to be copied. This includes copying material, ideas or concepts from a book,
article, report or other written document (whether published or unpublished), composition,
artwork, design, drawing, circuitry, computer program or software, web site, Internet, other
electronic resource, or another person’s assignment without appropriate acknowledgement.
• Paraphrasing another person’s work with very minor changes keeping the meaning, form
and/or progression of ideas of the original.
• Piecing together sections of the work of others into a new whole.
• Presenting an assessment item as independent work when it has been produced in whole or
part in collusion with other people, for example, another student or a tutor.
• Claiming credit for a proportion a work contributed to a group assessment item that is greater
than that actually contributed.
• Submitting an assessment item that has already been submitted for academic credit
elsewhere may also be considered plagiarism.
• The inclusion of the thoughts or work of another with attribution appropriate to the academic
discipline does not amount to plagiarism.
Students are reminded of their Rights and Responsibilities in respect of plagiarism, as set out in the
University Undergraduate and Postgraduate Handbooks, and are encouraged to seek advice from
academic staff whenever necessary to ensure they avoid plagiarism in all its forms.
The Learning Centre website is the central University online resource for staff and student information
on plagiarism and academic honesty. It can be located at: www.lc.unsw.edu.au/plagiarism
The Learning Centre also provides substantial educational written materials, workshops, and tutorials
to aid students, for example, in:
• Correct referencing practices.
• Paraphrasing, summarising, essay writing, and time management.
• Appropriate use of, and attribution for, a range of materials including text, images, formulae
and concepts.
Individual assistance is available on request from The Learning Centre.
Students are also reminded that careful time management is an important part of study and one of
the identified causes of plagiarism is poor time management. Students should allow sufficient time
for research, drafting, and the proper referencing of sources in preparing all assessment items.
20
Course Assessment – Detailed Instructions
A. Online Laboratory Safety Quiz – COMPULSORY
DUE: by 9am on the day of your first Practical Class
In order to be permitted to take part in laboratory classes, you must complete an online
Laboratory Safety Quiz that is accessed through the BABS1201 Moodle site. Prior to your
laboratory class, go to the BABS1201 Moodle site and enter the ‘Laboratory Safety Quiz’
module by clicking on the appropriate icon on the home page. Follow the instructions
provided there and use the above information on occupational health and safety that you
have discussed with your demonstrator today to complete the quiz. When you have finished
the quiz and submitted all your answers, you will receive a mark. If ANY of your answers
were incorrect, then you MUST attempt the quiz again and keep repeating this proceess until
you have scored 100%. Since it is crucial that you are aware of all important health and
safety rules and regulations, you can attempt the quiz as many times as required for you to
get ALL the answers correct. Your final quiz mark will be checked prior to your lab.
This quiz is compulsory, but does not comtribute to your grade.
If you have not scored 100% in the quiz by 9am on the day of your practical class you
will NOT be permitted to attend that lab class or any subsequent lab class until you
have satisfied this requirement.
21
B. Session Tests 1 and 2 – 10% each

Weeks 4 and 10 – online during your enrolled lecture time
Each test covers both theory and practical material. Test one includes from Weeks 1 to 4
(inclusive) of session. Test two includes Weeks 5-9 (inclusive).
The format of the exam is multiple choice questions.
The exam will be online, during your enrolled lecture time. Students that are unable to
access a device to complete either of these tests need to contact the course convenor at
least one week prior so that a venue / device can be organised.
More information about this test will be provided in lectures and via Moodle.
If you miss this test due to illness or misadventure, please apply for special consideration
online (see page 18 for instructions).
22
C. Science Communication Project
The Science Communication Project is a group assignment with multiple components that
runs throughout the session. The project focuses on advanced biology topics and aims to
develop, exercise and enhance your science communication skills. Working in a team of four
(4), students you will:
1. Select a topic from the list provided;
2. Perform a literature search on their chosen topic (see Moodle for a module on how to
conduct a literature search);
3. Write and submit an individual ESSAY (15%) that compares primary and secondary
scientific journal articles on their topic;
4. Meet regularly with your team to discuss findings on your topic, and develop a
presentation that effectively communicates the central biological concepts, especially
with respect to how those concepts align with BABS1201 course themes and learning
activity topics;
5. PITCH (5%) your presentation ideas to the larger laboratory group for peer feedback
on the design, biological content and feasibility of their project whilst providing similar
feedback to other project teams in the class;
6. Utilise the peer feedback received in the pitch to finalise your team PRESENTATION
(10%) on your advanced biology topic for submission and showcasing at the end of
session;
7. Submit a team PORTFOLIO (5%) that documents the proceedings of all team
meetings, including an inventory of ideas, team member roles, major decisions, and
other notes on the presentation design and execution;
8. Submit an individual REFLECTIVE SUMMARY (5%) that describes your personal

learning from both positive and negative experience throughout the duration of the
Project, including a peer evaluation of team member contributions to all components
of the project, and how any problems could have been better managed by the team.
This project incorporates the following UNSW Science graduate attributes:
• Research, inquiry and analytical thinking abilities;

• Capability and motivation for intellectual development;
• Communication;
• Teamwork, collaborative and management skills; and,
• Information literacy.
23
SUMMARY OF ASSESSABLE PROJECT COMPONENTS:
Assessable Assessment
Specific Learning Outcomes Due Date
Component Weighting
• Search for peer-reviewed scientific

literature
Scientific • Discriminate between primary and Practical 3
10%
Literature Essay secondary research papers (Week 6/7)
• Practice reflective writing and written
communication skills
• Effectively communicate ideas and Practical 4

Presentation
scientific concepts to peers 5%
Pitch (Week 8/9)
• Provide constructive feedback to peers
• Effectively communicate ideas and

scientific concepts to peers
• Use peer feedback to improve/enhance Practical 6
Presentation content and/or delivery of presentation 10%
(Week 11/12)
• Use creativity to develop and deliver an
accurate and effective scientific
presentation to peers
• Thoroughly and reliably record/document

team meetings/communications Practical 6
Portfolio • Maintain an inventory of all work 5%
pertaining to design, development and (Week 11/12)
delivery of scientific presentation
• Maintain a diary of personal learning

experiences gained throughout project
• Employ reflective practices to write about
personal responses to learning
Reflective experiences, opinions, events and new Practical 6
5%
Summary information (Week 11/12)
• Accurately document and fairly evaluate
contributions of individual team members
to the project
• Define learnt skills
Total Assessment Weighting: 35%

24
LIST OF PROJECT TOPICS:
After confirming the members of your Project team, you must collectively select a current
biology topic for your project from the list below. These topics have been carefully selected
for their alignment with core course concepts and for their feasibility for all components of
this assignment. It is possible that your team may be permitted to select a topic of interest
that is not on the list, but such topics must firstly be assessed and approved by your
demonstrator and/or course convenors.
1. The origin of blue eyes is a single human ancestor with a specific mutation in Herc
gene https://www.sciencedaily.com/releases/2008/01/080130170343.htm
2. The Tardigrade (water bear) genome has been sequenced and it’s even weirder than
we thought https://sciencealert.com/the-tardigrade-genome-has-been-sequenced-
and-it-has-the-most-foreign-dna-of-any-animal
3. A new mechanism of action of the Replisome means all the biology text books need
to be re-written http://www.labmanager.com/news/2015/11/study-reveals-the-
architecture-of-the-molecular-machine-that-copies-dna?fw1pk=2#.VjoxtyserSg
4. The science of genetic inheritance is weirder than we thought
http://www.sciencealert.com/watch-the-science-of-genetic-inheritance-is-weirder-
than-we-thought
5. Individuals with Aquagenic urticaria have an allergy to water
http://www.sciencealert.com/here-s-what-happens-if-you-develop-an-allergy-to-water
6. Gene-editing technique used to create low-gluten bread suitable for celiacs
http://www.iflscience.com/health-and-medicine/geneediting-technique-used-to-create-
lowgluten-bread-suitable-for-celiacs/
7. This biohacker became the first person to edit their own DNA
http://www.iflscience.com/health-and-medicine/this-biohacker-became-the-first-
person-to-edit-his-own-dna/
8. CRISPR gene editing tool used to treat genetic disease in an animal for the first time
http://www.sciencealert.com/crispr-gene-editing-tool-used-to-treat-genetic-disease-in-
an-animal-for-the-first-time
9. Is it ok to eat healthy food during the week and then binge on rubbish food on the
weekend? https://www.science.unsw.edu.au/news/study-weekend-binge-just-bad-gut-
regular-junk-food-diet-study-suggests
10. Do red heads have super powers? Does mutation in the MC1R gene also lead to
increased tolerance to pain in red haired individuals?
11. A protein found in human breast milk could help kill drug resistant bacteria
http://www.sciencealert.com/a-protein-found-in-human-breast-milk-could-help-kill-
drug-resistant-bacteria
12. Ketamine could be approved for treating depression http://www.iflscience.com/health-
and-medicine/ketamine-could-be-authorized-treat-depression
13. Do we all carry the genes for autism? http://www.sciencealert.com/we-all-carry-the-
genes-for-autism-study-finds
14. A vitamin has been found that halts aging in muscle tissues and increases life span
http://www.iflscience.com/health-and-medicine/awesome-vitamin-found-halt-aging-
muscle-tissues
15. Eating less improves mood, sleep and sex drive http://www.sciencealert.com/eating-
less-improves-mood-sleep-and-sex-drive-in-healthy-people-study-finds
16. The first eukaryotes without a normal cellular power supply have been found
http://www.sciencemag.org/news/2016/05/first-eukaryotes-found-without-normal-
cellular-power-supply?utm_source=sciencemagazine&utm_medium=facebook-
text&utm_campaign=noeukaryote-4260
17. Can the ‘RNA World’ be used to explain the origins of life?
http://www.sciencemag.org/news/2016/05/rna-world-inches-closer-explaining-origins-
life?utm_source=sciencemagazine&utm_medium=facebook-
text&utm_campaign=rnaworld-4268
25
18. Humans are still evolving and we can watch it happen

http://www.sciencemag.org/news/2016/05/humans-are-still-evolving-and-we-can-
watch-it-happen?utm_source=sciencemagazine&utm_medium=facebook-
text&utm_campaign=huvolution-4363
19. Could this new patent yield a functional cure for Type I diabetes?
http://www.sciencealert.com/a-patent-s-just-been-granted-for-what-could-be-a-
functional-cure-for-type-1-diabetes
20. Which health supplements are not backed by science?
http://www.iflscience.com/health-and-medicine/see-which-health-supplements-arent-
backed-by-science/
21. Scientists have found a woman whose eyes have a whole new type of colour receptor
http://www.sciencealert.com/scientists-have-found-a-woman-whose-eyes-have-a-
whole-new-type-of-colour-receptor
22. Scientists think they finally know why our genes are made of DNA and not RNA
http://www.sciencealert.com/scientists-think-they-finally-know-why-our-genes-are-
made-of-dna-not-rna
23. A brand new human organ has been classified http://www.sciencealert.com/it-s-
official-a-brand-new-human-organ-has-been-classified
24. Forget what you learned in high school – this new carbon molecule has 6 bonds
http://www.sciencealert.com/forget-what-you-learned-in-high-school-this-new-carbon-
molecule-has-6-bonds
25. Have scientists just announced our best shot at ending antibiotic resistance to date?
http://www.sciencealert.com/scientists-just-announced-our-best-shot-at-ending-
antibiotic-resistance-to-date
26. We might finally know what triggered living cells to evolve for the first time
http://www.sciencealert.com/scientists-might-have-discovered-what-allowed-life-to-
evolve
27. An epigenetics gold rush: new controls for gene expression
http://www.nature.com/news/an-epigenetics-gold-rush-new-controls-for-gene-
expression-
1.21513?WT.mc_id=FBK_NA_1702_FHNEWSFEPIGENETICSGOLDRUSH_PORTF
OLIO
28. An unexpected new lung function has been discovered and it could disrupt decades
of scientific thought http://www.sciencealert.com/an-unexpected-new-lung-function-
has-been-discovered-and-it-could-disrupt-decades-of-scientific-thought
29. Scientists have successfully reversed DNA aging in mice
http://www.sciencealert.com/scientists-have-successfully-reversed-dna-ageing-in-
mice
30. Two drugs have been identified that could halt the progression of neurodegenerative
diseases http://www.iflscience.com/health-and-medicine/two-drugs-identified-that-
could-halt-the-progression-of-neurodegenerative-diseases/
31. The energy generators inside our cells reach a sizzling 50°C
https://www.newscientist.com/article/2129849-the-energy-generators-inside-our-cells-
reach-a-sizzling-
50c/?utm_term=Autofeed&utm_campaign=Echobox&utm_medium=Social&cmpid=S
OC%7CNSNS%7C2017-Echobox&utm_source=Facebook#link_time=1493901004
32. Cell maps reveal fresh details on how the immune system fights cancer
http://www.nature.com/news/cell-maps-reveal-fresh-details-on-how-the-immune-
system-fights-cancer-
1.21931?WT.mc_id=FBK_NA_1705_FHNEWSIMMUNECELLS_PORTFOLIO
33. Antibody-powered nucleic acid release using a DNA-based nanomachine
https://www.nature.com/articles/ncomms15150
34. High intensity workouts could slow down your aging by almost a decade
http://www.iflscience.com/health-and-medicine/highintensity-workouts-could-slow-
down-your-aging-by-almost-a-decade/
35. First timeline of a cancer tracks tumours from origin to spread
https://www.newscientist.com/article/2130702-first-timeline-of-a-cancer-tracks-
26
tumours-from-origin-to-
spread/?utm_campaign=Echobox&utm_medium=Social&utm_source=Facebook#link
_time=1494933833
36. A diabetes drug may work by changing gut bacteria
https://www.newscientist.com/article/2132009-diabetes-drug-may-work-by-changing-
gut-bacteria-
makeup/?utm_campaign=Echobox&utm_medium=Social&utm_source=Facebook#lin
k_time=1495471397
37. A new study identifies 52 genes associated with human intelligence
https://www.facebook.com/nature/posts/10154856218303167
38. The brain starts to eat itself after chronic sleep deprivation
https://www.newscientist.com/article/2132258-the-brain-starts-to-eat-itself-after-
chronic-sleep-
deprivation/?utm_term=Autofeed&utm_campaign=Echobox&utm_medium=Social&c
mpid=SOC%7CNSNS%7C2017-
Echobox&utm_source=Facebook#link_time=1495578558
39. CRISPR kills HIV and eats Zika 'like Pac-man'. Its next target? Cancer
https://www.wired.co.uk/article/crispr-disease-rna-hiv
40. CRISPR gene editing can cause hundreds of unexpected mutations
http://www.sciencealert.com/turns-out-crispr-gene-editing-can-cause-hundreds-of-
unexpected-mutations
41. This Is the first ever nanoscale image of a living cell membrane. It's beautiful.
http://www.sciencealert.com/researchers-close-a-debate-with-a-nanoscale-image-of-
a-living-cell-membrane
42. Gastric bypass surgery gives patients a new set of helpful microbes
http://www.sciencealert.com/gastric-bypass-surgery-gives-patients-a-new-set-of-
helpful-microbes
43. Revolutionary tattoos designed to change colour according to your health
http://mymodernmet.com/dermal-abyss-biosensor-tattoos/
44. Is ADHD a sleep disorder? Stimulant drug improves symptoms
https://www.newscientist.com/article/mg23431283-100-is-adhd-a-sleep-disorder-
stimulant-drug-improves-
symptoms/?utm_campaign=Echobox&utm_medium=Social&utm_source=Facebook&
cmpid=SOC%7CNSNS%7C2017-Echobox#link_time=1496396954
45. Can gene therapy be used to switch off asthma? http://www.sciencealert.com/gene-
therapy-used-to-switch-off-asthma
46. Tea consumption leads to epigenetic changes in women
https://medicalxpress.com/news/2017-05-tea-consumption-epigenetic-women.html
47. Designer viruses successfully stimulate the immune system to fight cancer
https://www.technologynetworks.com/cancer-research/news/designer-viruses-
successfully-stimulate-the-immune-system-to-fight-cancer-289203
48. Lifelong protection from sever allergies could be possible with a new treatment
http://www.iflscience.com/health-and-medicine/lifelong-protection-from-severe-
allergies-could-be-possible-with-new-treatment/
49. 100 year old drug produces temporary improved learning skills in autistic children
http://www.iflscience.com/brain/100yearold-drug-produces-temporary-improved-
learning-skills-in-autistic-children/
50. Scientists discover plants have ‘brains’ that determine when they grow
http://www.iflscience.com/plants-and-animals/scientists-discover-plants-brains-
determine-grow/
51. This cancer drug proves to be effective against multiple tumours
https://mobile.nytimes.com/2017/06/08/health/cancer-drug-keytruda-
tumors.html?smid=fb-nytimes&smtyp=cur&referer=http://m.facebook.com
52. 5 kilograms of broccoli in a pill slashes diabetics’ blood sugar
https://www.newscientist.com/article/2134735-5-kilograms-of-broccoli-in-a-pill-
slashes-diabetics-blood-sugar/?cmpid=SOC%7CNSNS%7C2017-
27
Echobox&utm_campaign=Echobox&utm_medium=Social&utm_source=Facebook#lin
k_time=1497519098
53. A nine-year collaboration has just shown how sugar influences cancer cell growth
http://www.sciencealert.com/a-nine-year-study-has-just-shown-how-sugar-
exacerbates-cancer
54. New semi-synthetic organism can make molecules we’ve never seen before
http://www.sciencealert.com/new-semi-synthetic-organism-can-make-molecules-we-
ve-never-seen-before-dna-unnatural
55. Latest DNA analysis shows the Yeti are actually just a bunch of bears
http://www.sciencealert.com/dna-analysis-yeti-samples-asian-bears-no-proof-of-
cryptids
56. Babies who get more cuddles have their genetics changed for years
http://www.sciencealert.com/cuddling-babies-alters-their-genetics-dna-for-years
57. Living bacteria “From outer space” have been found on the outside of the ISS
http://www.sciencealert.com/living-bacteria-from-outer-space-found-clinging-to-iss-
alien-life
58. Poo pills really are becoming our answer to dangerous superbug infections
http://www.sciencealert.com/poo-pills-transplants-superbug-clostridium-difficile-
infection-cure-medical-trial
59. This protein in your brain could be at the heart of creating memories
http://www.sciencealert.com/rna-binding-protein-staufen2-linked-to-synaptic-plasticity-
learning-memory
60. World’s smallest tape recorder has been built inside a living bacterium
http://www.sciencealert.com/smallest-tape-recorder-crispr-cas-bacterium
28
PROJECT TIMELINE
Check Moodle announcements at least weekly for updates and supporting materials to guide
your project work.
Week 2/3 In Lab Class Practical 1:

• Form project groups
• Select project topic
• Schedule a meeting time and venue for your team in Week 3/4
Week 3/4 Individual (in own time):
• Team members should start individually researching their topic prior to their arranged
meeting time in Week 3/4. Initial research could simply involve internet searches
using your topic title and/or keywords within it. These searches may yield popular
science communications, links to various multimedia communications (e.g. tv/radio
excerpts, videos etc.), as well as papers from peer-reviewed scientific literature. All
are acceptable results for your initial research. As you progress through the Project
and related BABS1201 learning activities, you and your team members will become
more confident about which resources/sources of information to use for the essay
and presentation.
• Work through the ‘Scientific Literature’ lesson on Moodle. Other lessons on
conducting a literature search and referencing may also be useful.
Week 3/4 Team Meeting (out of class):
• Scheduled meeting team meeting
• Confirm topic and team members
• Discuss scientific literature essay and assign one primary and one secondary
research article to each team member for the purpose of completing the scientific
literature essay.
• Consultation with tutor - Confirmation of Project team members and chosen topics.
• Scheduled team meeting.
• Team members should continue to research their topic, with a focus on peer-
reviewed scientific literature (i.e. journal articles).
• Start developing ideas for the content and format of your major presentation (see
assignment guidelines below; presentation ‘pitch’ is due in Week 8/9 and final
presentation is due in Week 12/13)
• Each team member should be individually researching and writing their “scientific
literature essay”
• Consultation with tutor
• Scheduled meeting team meeting.
• Develop a brief 3-5 minute project ‘pitch’ that encapsulates the fundamental elements
of your presentation plan (see below for pitch guidelines). You will pitch your
presentation plan to the rest of your demonstrator group in the next laboratory class
(Week 8/9)
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• Each team member should continue with their individual scientific literature essay
(due in next lab class, Practical 4).
• Project Presentation Pitches delivered in lab class. Your demonstrator will facilitate
both the individual team pitches and the peer feedback sessions after each pitch
• Individual scientific literature essays due in this lab class. An electronic copy should
be submitted online in Moodle and a hard copy should be given to your
demonstrator at the beginning of class.
• Scheduled meeting team meeting
• Continue with the plan for your team presentation
• Consultation with tutor
• Finalise the plan of your presentation that details its format and indicates how
individual presentation criteria (see details below) will be satisfied.
• Finalise your team’s portfolio for submission in Week 12/13
Week 11/12 Individual:
• Start compiling your personal Reflective Summary and Peer Evaluations (see below
for guidelines) for submission
• Project Final Presentations. Submit your teams’ presentation onto Moodle as a
single file.
• Each team will have a maximum of 5 minutes to showcase/highlight their
presentation to the whole lab class. The teams will select one spokesperson for the
showcase
• Your demonstrator will help facilitate the presentations for your group.
• Team Portfolios due.
• Individual Reflective Summary due. See below for guidelines.
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Scientific Literature Essay – 10%
Your individual essay is due at the start of Practical 3

(Week 6/7). Essays will be handed in during class and submitted via Turnitin on Moodle.
Check Moodle announcements regularly for announcements.
In the first phase of the Project, you will be assigned to a team of approximately 4 members. As a
team, you will select a current biology topic from the list provided (or an alternative current biology
topic that has been approved by course convenors). The first phase of the Project will involve doing
some individual research on your topic and then reporting back to your team for discussion. Your initial
searches may yield different kinds of information, including news articles, popular science
communications, videos and television program segments, as well as peer-reviewed scientific journal
articles. Since scientific journal articles will be the most difficult to understand for non-experts, we
recommend that you start by looking at alternative sources of information. Then, once you have a
better understanding of your topic, we then encourage you to start looking at the peer-reviewed
scientific literature. The Scientific Literature Essay described in this section relates directly to the peer-
reviewed scientific literature that you and your team members find on your topic.
This assignment is designed as a first university writing assignment. It will be followed by other
assignments in this course, and in other courses, that will progressively introduce you to the demands
of scientific report writing or literature reviews. This assignment, is a more personal piece of writing
which in part reflects upon your own experience locating and reading a scientific article.
The objectives of the task do not focus on an understanding of the scientific literature. A major
objective is to see if you can write clearly and concisely about biology. If, as a result of this
assessment, we think you have problems writing, we will refer you to the UNSW Learning Centre for
assistance.
The essay should be approximately 1000 words long, excluding references. You must perform a word
count and indicate the count at the begnning of your essay. You will not be penalised for going slightly
over 1000 words, but penalties will apply to essays that exceed the limit by more than 5%.
From information presented in BABS1201, you should become familiar with the different types of peer-
reviewed literature used by the scientific community. One of the major objectives of this assignment is
to ascertain whether YOU are able to differentiate between primary and secondary (review) journal
articles, so your demonstrator or lecturers will NOT provide you with an answer if you ask them to
check the articles you are considering. They will, however, discuss HOW to differentiate between the
two in class.
ESSAY INSTRUCTIONS
Your essay task is to find a REVIEW article (ie. secondary literature) from any biological science
discipline, and then from the cited literature that is mentioned in the review, select one PRIMARY
research article. Your essay must include and will be assessed on the following criteria:
1. A simple description of the nature of the review article. This should include a description of the
topic that is being reviewed as well as a description of the audience for which the review has
been written. This will require you to reflect upon the journal, and the audience that the journal
is typically written for. What is the discipline, for example, is it zoology, microbiology, genetics
or something else that you think best describes the work? Remember that there may be more
than one discipline name that you can think of, and you could discuss the different possibilities
if that is the case. You should say a little bit about what you think the discipline is about. Of
course you do not have space to do this in any detail. In some cases it may be easy. In others,
the boundaries of the discipline may be unclear to you. Feel free to discuss your uncertainties.
Remember that this is a reflective essay.
31
2. A description of the journal. Write about the relationship between the journal you have chosen
and the discipline. In some cases, this will mean you will find out a little about a professional
society that is associated with the journal. The journal may be a general one, which ‘serves’
many disciplines, or may be a journal that is strongly associated with a particular scientific
sub-discipline. The journal may target regional, national or international audiences.
3. Identify one PRIMARY research paper from the reference list of your review article. Locate
and read through a primary research article selected from the citations in your review article.
Briefly describe the article in your essay and discuss its role in or contribution to the review
article. This article should be cited in your own reference list for your essay.
4. A description of the purpose of the primary article and a brief summary of the results of the
investigations that are reported within it. What was the main outcome? Why is it significant?
Don’t get bogged down with the detail, focus on the main points only. You may not understand
very much and that is okay – you are a first year biology student and the article may be written
for an audience of specialised researchers. If this is the case, do not panic! You will not be
penalised as long as you can write a sensible reflection eg. what was interesting? what did
you learn? what was difficult to understand? etc. (Remember this is a reflective essay, where
you are free to discuss both your success and difficulties!) This part of your essay could look
something like this: “I chose this article as I am interested in Australian animals, and this paper
was about the behaviour of wombats. However, it much of it was difficult to understand. The
page included 15 words that I had never seen before. Although I used a dictionary to clarify
the meaning of most of the words, I was still unable to make any sense of the article as I had
no general knowledge of animal behaviours, such as foraging and being territorial, that this
article built on etc.”
5. What was the aim / hypothesis investigated in the primary article? The Scientific Literature
lesson on Moodle steps you through the parts of a journal article and will help you identify
where to look for this. Which section did you find the aim/ hypothesis, and can your write it in
your own words, suitable for a BABS1201 audience rather than an expert?
6. A sentence or two on your understanding of the nature and purpose of primary literature
compared to secondary literature. Well scoring essays will be able to explain how their primary
article contributed to the review article.
You must carefully read the above points and address them. Omitting to include one of the criteria will
result in a loss of marks. The clarity of your writing is also important, so ensure you leave sufficient
time to proof read your work. Remember that you can score full marks without understanding the
journal articles if you just follow the instructions above.
Please note that you MUST REFERENCE both the review article and primary research article (and
any other articles you use) at the end of your essay so markers can assess your essay accurately.
This does not mean you include the references cited within the two articles ie. do NOT paste in the
references section from your two articles, only provides details of references you use, simply reference
correctly the two articles. A module on how to find and reference scientific articles correctly is available
on Moodle.
Write as if your reader is another BABS1201 student, this means that your descriptions of the science
need to be in your own words. All assignments will be screen for plagiarism, so it is particularly
important.
32
D. Mastering biology – 5%
11:59pm on Friday of Weeks 4, 8, 9, 10 and 13
In weeks 3, 7, 8, 9 and 12 you will be provided access to an online quiz related to the concepts
learned during the practical component of the course. Each quiz is worth 1% of your final assessment
and should take you less than 30 minutes to complete (although it is not timed). The quiz will be
accessable via Moodle on the week of the relevant practical and is due by the end of the following
week (11:59pm on Friday of week 4, 8, 9, 10 and 13 respectively).
E. Final Theory Exam – 40%

Date, Time and Venue to be Advised
The final examination is conducted externally during the UNSW June examination period. The exam
can address ANY material covered in lectures and practical classes throughout the BABS1201
program. The format and weighting of questions in the final exam will be shown on the front cover of
the exam paper, which will be posted on Moodle after submission to the exams branch part way
through this session. PLEASE NOTE that the final exam is a COMPULSORY assessment and must
be completed in order to satisfy the requirements for passing the course. If you miss this exam due to
illness or misadventure, please apply for special consideration online (see page 18 for instructions).
Please note that there are NO PAST EXAM PAPERS provided in this course. The best ways to study
for the above tests and exams are to revise your lecture notes and corresponding learning outcomes,
using the mastering biology and other revision acvitvies provided for you via moodle and access any
resources that are referenced, including your recommended text for the course.
33
INTRODUCTION TO LABORATORY SAFETY
CONTENTS
1. Health & safety guidelines

2. Online Laboratory Safety Quiz
3. Mastering Biology
OBJECTIVE
• Be aware of safe work practices in the laboratory.
UNSW Science graduate attributes:
• Capability and motivation for intellectual development

• Ethical, social and professional understanding
1. HEALTH & SAFETY
In your first laboratory class you will meet your laboratory demonstrator, and be
introduced to the basic principles of laboratory safety. This is a requirement of the
Health and Safety legislation. At the end of the class, you will be required to sign a
declaration that states that you have read and understood the rules. If you fail to do
this, you will not be permitted to participate in further practical classes. Some basic
guidelines are provided below, and a video on laboratory safety is available on
Modle.
General conduct
A laboratory is intended for serious work and students are expected to behave
appropropriately.
Students must read the instructions to their experiments carefully before starting
work, and should be aware of all possible hazards.
No undergraduate students are to work in the laboratories outside class hours
without permission and supervision.
All accidents and injuries must be reported to the lecturer or demonstrator in charge
of the practical class, so that treatment may be provided if necessary and the incident
reported.
34
Evacuation
If there is a fire or other major calamity an alarm will sound. Messages may be
broadcast from the university’s Emergency Response group. Unless there is an
immediate danger nearby, when you first hear the initial ‘Prepare to Evacuate’ alarm,
stop what you are doing and wait for further instructions.
Follow the instructions from your lecturer or demonstrator. Close all the doors and
windows if possible. Quickly check to see that everyone is out of the room. Move
steadily to the exit. If for some reason, you are not in the groundfloor labs, move
quickly to the nearest stair well and out of the building. Do not use the lifts.
Assemble in the Michael Birt Gardens in front of the Chancellery Building (near
Gate 9 on High Street). Supervisors should bring the class roll and check that every
one has left the building.
Risk assessments
Working in a laboratory is inevitably associated with certain risks. Good laboratory

practice means working in such a way as to eliminate, or at least minimise, these
hazards. In order to perform your work safely and to comply with government
legislation's, a risk assessment has been conducted on all of work performed in each
practical class and is included in the manual. The risks are categorised as follows:
Biological hazards: Such as microorganisms used in an experiment.
Chemical hazards: Most of the chemicals used in this subject are not hazardous at
the concentrations that are being used, however appropriate PPE (eg. lab coat,
closed shoes) should be used in the laboratory at all times. Some practicals employ
hazardous chemicals. In these cases the hazard and precautions required are
described in the instructions for the class, and may be updated by your demonstrator.
Safety Data Sheets (SDS) are available for all of the hazardous chemicals from your
demonstrator.
Physical hazards: Heat sources, such as water baths, breakable glassware, sharp
objects such as plastic tips and razor blades.
Hazards involving work environments: This include ergonomics eg. the chair and
desk position you use in the laboratory.
Some guidance to working safely in the laboratory is provied below. You also need to
watch the video on laboratory safety before class, and your demonstrator will discuss
the particular issues related to you laboratory classroom and the experiments with
you.
It is imperative that you be present at the beginning of each class to ensure that you
are available to review safety procedures. If you are not present for this you will be
excluded from the class and marked as absent. Below are some guidelines that you
must follow which will ensure good laboratory practice and minimise the
consequences of risks:
35
Some specific guidelines:
• A laboratory coat must ALWAYS be worn while in the lab, and removed
before leaving the laboratory. Where necessary (as advised by your
demonstrator), protective gloves and safety glasses should also be worn.
• Gloves will be provided and MUST be disposed of in the designated ‘Scientific

Waste’ bins and NOT the general waste bins. DO NOT wear lab coats or
gloves outside the laboratory!
• Adequate protective clothing also includes footwear. Fully enclosed, non-

absorbant shoes must be worn at ALL times.
• Long hair must be tied back or up whilst you are in the laboratory.
• You must not eat, drink, apply make-up etc. in the lab. Neither should you
bring food, drink etc. into the lab. Never leave food or drink (water bottles
included) on laboratory benches! Habits such as chewing the ends of pens
and pencils, nail biting etc. are often difficult to avoid, but you should make a
conscious effort not to do them.
• Do not sit on laboratory benches.
• All bags and/or extraneous clothing items must be stored UNDER benches
and NOT on benches or on the floor between the benches where they could
act as a tripping hazard.
• Do not invite anyone into the lab. They may not be aware of the hazards and
may themselves create additional hazards.
• If there is an accident ask a fellow student to call someone in authority

immediately. If there is a fire, remove yourself from immediate danger and call
someone in authority immediately. If there is a small spill of a non-toxic or
harmless chemical or solution such as water, you should clean it up yourself or
check with your demonstrator first for the best way to proceed.
• Before leaving the laboratory, tidy your bench, clean your bench area and
ALWAYS wash your hands.
• If you feel discomfort from your work (eg. heat exhaustion or back pain),
consult your demonstrator.
36
Using your knowledge of safe work practices in the laboratory, circle the
problems in this picture:
Figure from: Baker, M. (2016) How quality control could save your science. Nature 529, pp
456–458 doi:10.1038/529456a
You must sign the declaration below and have it witnessed by a tutor or demonstrator before
you will be permitted to take part in practical classes.
I, …………………………………….............................. ........………………………...............
name student ID
certify that I have read and understood the Safety in Laboratories information above, and
agree to abide by these rules at all times when in University Laboratories.
Tutor: ………………………….................................. ........................................................

name signature
37
2. ONLINE LABORATORY SAFETY QUIZ
In order to be permitted to take part in laboratory classes, you must also complete an
online Laboratory Safety Quiz that is accessed through the BABS1201 Moodle site.
When you have finished the quiz and submitted all your answers, you will receive a
mark out of 12. If ANY of your answers were incorrect, then you MUST attempt the
quiz again and keep repeating this proceess until you have scored a mark of 12/12
(that is, 100%).
Since it is crucial that you are aware of all important health and safety rules and
regulations, you can attempt the quiz as many times as required for you to get ALL
the answers correct.
If you have not scored 100% in the quiz by 9am on the day of your practical
class you will NOT be permitted to attend that lab class or any subsequent lab
class until you have satisfied this requirement.
3. MASTERING BIOLOGY
The purpose of the following exercises is to familiarize you with the system you will
be using for the rest of your course. These exercises are not intended to teach or
test your knowledge of any specific subject material. Therefore, you will not be
penalized for using hints or submitting incorrect answers. Accessing Mastering
Biology is via Moodle, and is demonstratored in your first lecture.
Items in Mastering Biology typically have an introduction, possibly figures or

animations, and one or more parts for you to answer.
1. Navigate to the Mastering Biology via Moodle and complete the activity named
“Introduction to Mastering Biology”.
2. If you have any trouble running the exercises you may need to adjust your
browser settings, see here:
http://www.pearsonmylabandmastering.com/northamerica/masteringbiology/syst
em-requirements/index.html
3. Ensuring Mastering Biology works is your responsibility BEFORE your
assessable quizzes commence. If you encounter problems, the course
administrator or conveners will ask that you:
- Have checked you have the correct system requirements
- Have complete the “Introduction to Mastering Biology” module
- Have accessed the Mastering Biology 24/7 help desk via Moodle
38
SECTION 1:
PRACTICALS 1-2
EXPLORING CELL STRUCTURE
These two laboratory classes explore aspects of cell structure and concepts that will
be discussed in lectures. You will also practice some of the techniques we use to
explore cells.
The aims for this section are:

• Work safely in the laboratory.
• To competently use the light microscope (set up and care of the microscope).
• To report on microscopic structures observed through a light microscope
(drawing observations and measuring size).
• To identify key differences between internal structures of bacterial and
eukaryotic cells using the light microscope
• To competently perform basic staining procedures and light microscopy of
different types of cells
• To identify an unknown cell type and describe your findings, including:
- identifying the type of cell (bacteria, eukaryote, plant or animal);
- describing the procedure used to identify the cells (such as the type of
stain);
- describing the characteristics of the cells that enabled you to identify
them (organelles, size, and structures).

• Research, inquiry and analytical thinking abilities
• Communication
39
BABS Teaching Laboratory Practical 1: Cell Structure 1
Student Risk Assessment

BABS_RA_BABS1201_1
Hazards Risks Controls

Follow demonstrator’s
Biological agent (Environmental Infection instructions when handling
samples – pond water) biological agents.
PPE (lab coats, closed in shoes,
Biological agent Spills goggles & gloves as required).
(Microorganisms, Bacillus Adhere to aseptic techniques.
megaterium) Notify demonstrator immediately
Cuts from broken glass of any spills or other incidents.
Biological agent (Environmental Carry slides/coverslips in
samples – Spirogyra) suitable containers and dispose
of any broken/used items
Razor blades, glass immediately in sharps
slides/coverslips containers provided.
Proper handwashing with
antibacterial handwash before
leaving the laboratory.
Electrical Equipment Electric shock/ electrocution Avoid water/spillages when
(microscope) Exposure to biological agents working with electrical items. All
(see above) equipment regularly tagged and
tested by UNSW staff.
Postural damage from extended Maintain good posture at all
Ergonomics periods of time working at times whilst working at the
microscope or bench microscopes and computers. Do
not work at the microscope
/computer for more than two
hours without taking a break.
Personal Protective Equipment
Emergency Procedures
In the event of an alarm sounding, stop the experiment, turn of electrical equipment and wait for
confirmation from demonstrators to evacuate. Then pack up your bags and wash your hands. Follow
the instructions of the demonstrators regarding exits and assembly points. The BioScience assembly
point is in the lawn in front of the Chancellery. In the event of an injury inform the demonstrator. First
aiders and contact details are on display by the lifts.
Clean up and waste disposal
All used microfuge tubes should be placed in the biohazard bins. Used test tubes should be placed in
the appropriate container on the front bench of the lab. All solutions should be placed in the
appropriate liquid waste containers. Used slides and cover slips should be placed in approved
biohazard sharps containers.
Declaration – will be checked by demonstrator at the beginning of the practical class.

I have read and understand the safety requirements for this practical class and I will observe these
requirements.
Signature:……………………………………………………………Date:……………………………
Student number:………………………..
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PRACTICAL 1
CELL STRUCTURE I
LOOKING AT CELLS USING THE LIGHT MICROSCOPE
CONTENTS
1. Light microscopy
2. Observing microscopic life
3. Structure of a bacterial cell
4. Comparison of size of eukaryotic and bacterial cells
BEFORE ATTENDING THE LABORATORY CLASS:
Complete the Health and Safety quiz on Moodle.

Complete the ‘Introduction to Lab safety’ section in the Course Manual.
Complete Pre-lab quiz 1 on Moodle.
Read through the notes and ensure you know how to set up a microscope.
Watch the video on setting up a microscope.
Check that you know how to access the Mastering Biology Quiz 1 ‘Prokaryotic
versus Eukaryotic Cell Structure’ and know the due date. The quiz is worth 1% of
your final assessment and should take you around 15 minutes to complete.
OBJECTIVES
At the end of this practical class you should be able to:
• Work safely in the laboratory.
• To competently use the light microscope (set up and care of the microscope).
• To report on microscopic structures observed through a light microscope

(drawing observations and measuring size).
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1. LIGHT MICROSCOPY
Light microscopes are a powerful tool for identifying and examining single cells or
tissues. While there are many other techniques that can be used in conjunction with
light microscopy, such as electron microscopy, DNA fingerprinting and biochemical
techniques, light microscopes are still a crucial element of our scientific armoury, and
are widely used.
Examples:
• Hospital laboratories will look down a microscope to help identify a bacterial
species, such as Meningococcus, that is causing illness.
• Pathology laboratories will look at blood cells down a microscope to identify
leukaemia’s, or tissue samples to identify other cancers.
• Ecologists may look down a microscope to identify the microscopic organisms
present in the environment that can indicate the presence of pollution.
• Botanists use microscopes to identify seeds that are fertile.
• Biotechnologists may look down a microscope to identify cells that have
successfully been engineered to express a desired protein.
The characteristics of individual organisms that can help identify them include size,
shape, and internal structures. You can also use chemical stains to colour the
organisms which can provide even more information. So knowing how to get the
most out of your light microscope is a skill that you could need at many stages of
your future career.
The compound light microscope:
The compound light microscope is a precision optical instrument designed for

producing magnified images of objects using two or more glass lenses. The term
“light” refers to the fact that light transmits the image to your eye, in contrast to
‘electron microscopes’ in which beams of electrons are used to create magnified
images. “Compound” deals with the microscope having more than one lens.
“Microscope” is a word created from "micro" meaning small and "scope" meaning
view.
The key factor in optimising the compound light microscopes performance is not
magnification, but resolution. Resolution is the ability to separate two closely spaced
items. A lens magnifies by bending light. Optical microscopes are restricted in their
ability to resolve features by a phenomenon called diffraction which, based on the
nature of the optical system and the wavelengths of light used, sets a definite limit to
the optical resolution. Due to the diffraction of light, even the best optical microscope
is limited to a resolution of 0.2 micrometers (µm). In other words, the smallest detail
that can be seen under the highest magnification of the light microscope is 0.2 µm.
When using the 100X lens the light is bent at such an angle as it passes from glass
into air that it is impossible to properly or clearly observe the specimen. To prevent
the light being bent away on an angled path from the objective lens, immersion oil is
used. Immersion oil has the same refractive index as the glass, so light travelling up
through the slide, the oil and then the objective lens, is not refracted again until it
passes from the convex upper surface of the lens into the air above.
42
That bending, however, is what the lens is designed to do, sending the rays which left
the specimen at angles up the tube at new angles, to be resolved and magnified by
the ocular lens.
The oil immersion lens (100X), when used with a drop of oil, prevents this refraction
or deflection of angled light from its straight path as would occur if the light were to
pass at an angle from glass into air.
To use the oil immersion lens (100X), a drop of immersion oil is placed on the
specimen and the oil immersion objective (100X) is then lowered into the oil.
Please note that immersion oil must not be used with any other lens (4X, 10X, 40X),
as these lenses are not designed to come into contact with immersion oil, and the
use of oil will result in damage to the lens.
Parts of the light microscope:
There are many makes and models of light microscope. However, all light
microscopes are fundamentally the same, have similar controls and functions. The
microscope illustrated below is typical of the light microscope you will use in class.
43
3. Setting up the light microscope
In class video: How to set up a microscope
It is easy to view specimens with a microscope, but it is more difficult to obtain the
best view possible. The following section takes you through a step-by-step process
that will optimise the performance of the microscope for your eyes.
When you look through the eyepiece, try to keep both eyes open. If you have trouble,
cover one eye with your hand. But commit yourself to keep trying. You must
eventually be able to keep both eyes open.
1. Switching on microscope
Turn the power switch on (1).
Move the voltage control slide (2) to

set the light intensity.You should not
need to set the intensity to the
maximum power.
2. Specimen placement
Open the spring-loaded finger of

the specimen holder (1) and insert
the slide that is provided for each
student.
3. Focus
Swing in the 4x objective (1).
Using the coarse adjustment (2), raise

the stage as high as possible. Bring the
specimen into focus by lowering the
stage, using first the coarse and then
the fine adjustment knobs.
Swing in the 10x objective and refocus

using the coarse and/or fine adjustment
knobs.
44
4. Interpupillary distance
Looking through both eyepieces,

move the knurled dovetail slides until
a suitable binocular image is obtained.
5. Diopter adjustment
To achieve maximum binocular clarity, an

adjustment can be made to compensate
for differences in the vision of your left and
right eyes. Look at the image through the
right eyepiece with your right eye, and
focus on the specimen with the fine focus
adjustment.
Looking at the image through the left

eyepiece with your left eye, rotate the
diopter adjustment ring (1) to focus on the
specimen without using the focus
adjustment knobs.
6. Adjusting the height of the condenser
Raise the condenser using the condenser

height adjustment knob (2) until it is as
close to the slide as possible. Then lower
the condenser until the ‘pearly’ image of
the ground glass of the lamp unit is
sharply visible in the field of view. Now
readjust the focus to put the condenser
slightly out of focus – the ground glass
surface should just disappear.
The condenser can only be focused
correctly when the object on the slide is
itself in focus.
7. Objective change
Swing in the 40x objective to examine

your slide at relatively high
magnification. Ensure that the
nosepiece is clicked into position.
45
8. Condenser iris diaphragm adjustment
Turn the diaphragm lever (1) to vary the

diaphragm opening. This allows you to
adjust the contrast of your image.
Evaluating your microscope set-up:
Once your microscope is set up to your satisfaction, leave it on 40X objective, and
have your tutor/demonstrator check it.
Microscope adequately adjusted
Oil immersion
When you need higher magnification….
The 40X objective gives you about as good a magnification as you can get with a
lens-in-air. Higher magnification just gives you larger, blurred images. However,
resolution at higher magnification (100X objective) can be achieved if light from the
specimen passes to the lens through clear oil rather than air, because light scattering
at an oil/glass interface is less than at an air/glass interface. The oil immersion lens
(100X), when used with a drop of oil, prevents refraction or deflection of angled light
from its straight path that would occur if the light were to pass at an angle from glass
into air. The degree to which the light is refracted or bent by a substance is
formulated as its refractive index. As you might expect, the numerical aperture of a
lens, the light-function constant you used to calculate the resolution, is determined in
part by the refractive index of the glass.
To prevent the light from being bent away on an angled path from the objective lens,
and to allow the maximum amount of light from the specimen to be gathered by the
objective, a drop of immersion oil may be placed on the specimen and the 100x oil
immersion objective can then be lowered into the oil.
Immersion oil has the same refractive index as the glass, so light traveling up through
the slide, the oil and the objective lens is not refracted again until it passes from the
convex upper surface of the lens into the air above. That bending, however, is what
the lens is designed to do, sending the rays which left the specimen at angles up the
tube at new angles, to be resolved and magnified by the ocular lens.
46
As light strikes the specimen the qualities of the light are changed in several ways
that give the visual image we perceive. It may be scattered or reflected away from
a path leading to the objective, darkening the image; it may be completely occluded
by solid structures that appear black to the observer; specific wavelengths of the
light may be partially absorbed by certain substances (including stains), giving a
characteristic colour to the structures containing them.
Microscopy trouble shooting
Apparent fault Possible cause Correction

Power (lamp) not on or Turn power on & check
turned down too low voltage
Field dark Condenser diaphragm Open diaphragm
closed
Lamp filament burnt out Replace lamp
Colour of objects Condenser diaphragm Open diaphragm
indistinct closed too far
Poor resolution Condenser either too far Adjust condenser
open or too far closed diaphragm
Cover-slip too thick Replace
Slide up-side down Invert slide
Focusing attempts too Use fine focus and adjust
Unable to focus on rapid more slowly
object Objective has insufficient Use higher power
resolving power
Objective covered with Clean with lens tissue and
dried immersion oil from solvent
previous use
Dirt on eye lens of ocular
Specks in field of view Dirt on condenser lens Clean with lens tissue
Dirt on filter
Moving shadows in field Air and/or water bubbles in Remove oil with lens
immersion oil tissue. Re-apply
No oil contact between oil Adjust with course /fine
Light suddenly reduced immersion objective and focus control
slide
Calculating the total magnification of an image that you are viewing through the
microscope is really quite simple. To get the total magnification, take the power of the
objective (4X, 10X, 40X) and multiply by the power of the eyepiece to give total
magnification.
If you are looking at something through the 40X objective, what is the actual
magnification of the object you see?
47
Measurements and scales when using microscopes:
Often it is sufficient just to know an approximate measurement of the size of the

object you are viewing, i.e. whether it is about 10 µm or 10 mm in diameter. And it is
important to realize that the apparent size of the specimen will naturally depend on
which objective lens you are using to view it.
A good way to obtain an estimate of the size of the object is by comparing it to the
diameter of the field of view.
The diameter of the field of view is dependent on the magnification of two lenses - the
eyepiece lens and the objective lens. Since the eyepiece lens remains unchanged,
we can take the diameter of the field of view of the eyepiece and modify it for the
various objective lenses. The field number of the eyepieces you will be using is
18mm.
To calculate the true diameter of the field of view with different objectives, we use the
formula:
diameter = field number

objective magnification
So, using the 10X objective:
diameter = 18 = 1.8mm
10
Therefore an object on the slide which occupies half the field of view will measure
approximately 0.9mm or 1mm across.
Accurate measurements using the eyepiece scale
In order to provide an accurate scale for a drawing it may be necessary to have

accurate measurements. A ‘ruler’ or micrometer is built into the eyepiece of your
microscope. A microdot slide of the number ‘5’ has been provided as a trial slide.
PLEASE NOTE: make sure that your slide is positioned with the correct side
facing upwards. If you cannot focus on the number ‘5’ at higher objectives, you
may have the slide upside down! With this slide on the stage and in focus, observe
the eyepiece micrometer. Notice that the scale has 100 divisions.
Starting with the lowest power, move through the different non-oil objectives and note
that the size of the ruler does not change. However the apparent size of the ‘5’
changes with each new objective lens used. Therefore the divisions of the ruler
include a different amount of the ‘5’ with each different objective.
The high quality of your microscope lenses is such that calibration made at the
factory are good for all microscopes of the same model.
48
The values are:
4X objective each eyepiece scale division = 25 µm

10X objective each eyepiece scale division = 10 µm
40X objective each eyepiece scale division = 2.5 µm
100X objective (oil) each eyepiece scale division = 1 µm
You can get an accurate measurement of any object on a slide at any magnification.
Test this by measuring the ‘5’ on the microdot slide.
Using the scale, how high and how wide is the ‘5’ ?
Now you know the size of the object seen through your microscope. However
someone looking at a drawing you made of it will have absolutely no idea of its actual
size unless you also include some indication of size. This is done by placing a scale
on the drawing. The image below demonstrates how this may be done by showing a
bacterial cell and a scale bar indicating 500 nm.
Image: Raul Gonzalez and Cheryl Kerfeld (http://www.kerfeldlab.org/images.html)

Creative Commons
49
2. OBSERVING MICROSCOPIC LIFE
Experimental procedure:
1. Obtain a small sample of the pond water provided.
2. Place a drop on a clean microscope slide, and gently lower a coverslip onto the
slide as shown in Figure 1 below. This provides some protection for your
specimen. It prevents the specimen drying out, and it allows you to place oil on
top of the coverslip when you wish to use the oil immersion lens Be careful not to
squash your specimen.
Figure 1: Placing a coverslip on a slide.
3. Look at your slide under low power.
How many different types of organisms can you see?
How many are unicellular and how many multicellular?
Can you tell whether they are plants or animals? What characteristics might help
you decide?
Some common protists:
Protists are an informal term that describes a heterogeneous group of living things,
comprising those eukaryotes, which are neither animals, plants, nor fungi. Most
protists are unicellular eukaryotic cells, resembling animals and plants, and differing
from bacteria, for they have at least one well-defined nucleus. If your pond water
slide did not contain any protists, please take time to examine some of the fascinating
50
organisms that have been grown in the laboratory for you. Hopefully we will have
living specimens of Amoeba, Euglena and Paramecium for you to examine. These
are not easy organisms to maintain in a lab culture, so we may have to substitute
other species. Look at the demonstrations of pond water organisms that are set out
around the lab.
Paramecium are 'ciliates' (protists that use cilia for locomotion). Sometimes we have
a species which is decidedly green. The green colour comes from the chloroplasts of
symbiotic green algae that live within the Paramecium.
Amoeba is a genus of rhizopods (protists that use pseudopodia for locomotion).

These are fascinating organisms to watch.
Euglena is a genus of green flagellates (protists that use a flagellum for locomotion).
They are green because they contain chlorophyll and therefore can live by
photosynthesis. However, if placed in the dark they can also feed by ingesting food
particles.
Drawing your observations:
Drawing remains an important method of recording biological observations. It is also

a useful thing to do since it encourages the observer to look more carefully at the
specimen. You do not need to be artistic, just accurate and clear.
Make sure you recognise and label important characteristics of the cells you see.
This record might help you identify unknown cell types in later weeks e.g. organelles,
membranes, size, etc.
Outline drawings:
These drawings show relationships between parts of the subject, but provide little
detail. When using a microscope, line drawings are usually made to record what is
seen with the low power objective lens. See Figure 2 below as an example.
Figure 2: Paramecium 100x magnification

51
High power drawings:
These drawings are made with the use of high power objective lenses and show
individual cells. High power drawings may also show intracellular detail. To see any
structure within a cell requires a high power objective lens, usually with oil immersion.
See Figure 3 below.
Figure 3: Paramecium 1000x magnification (oil immersion)
These two types of drawing can be combined in order to show high power detail in
only a section of a specimen being illustrated. It would be extremely time consuming
to show details of individual cells throughout a drawing of a large section, so it may
be better to do a detailed drawing of one part only. In this case, the section which is
to be drawn in detail must be clearly defined on the outline drawing.
When making drawings of microscopic specimens, many people prefer to use one
eye to look down the microscope with the other eye focused on the drawing paper
placed at the side of the microscope. With a bit of practice it is possible to draw and
look down the microscope simultaneously. Always draw what you can see, not what
you think you should see. You will find that habitual accurate drawing will increase
your powers of observation. All drawings should be completed in class. Never make
a rough sketch and smarten it up later. This always leads to inaccuracies.
Make your drawings large and clear using the space provided. Drawings should be
made with a sharp HB pencil and the lines should be continuous. Never draw with
pen or coloured pencils.
52
Where specimens have repetition of detail it is best to make an outline sketch of the
whole specimen or field of view and then illustrate a clearly defined part of this sketch
with a separate detailed drawing as illustrated in figures 2 and 3.
• Label the drawings and diagrams fully in pencil.

• Keep your labels horizontal and to the side of the drawing, and rule lines to the
appropriate parts.
• Do not use arrowheads.
• Provide a title for each drawing.
• If notes are necessary as part of your observations, place them at the bottom
of the drawing or near the appropriate label. This allows a combined record of
structural and functional observations.
• There should be a scale with each drawing to indicate size.
Your observations:
Make line drawings as Figures 4 and 5, and work out the actual size of any two of the
organisms you see down your microscope.
Figure 4:
53
Figure 5:
3. STRUCTURE OF A BACTERIAL CELL
Bacterial cells have a much simpler structure than eukaryotic cells, and lack a
nucleus or organelles. They are also usually smaller, although in this practical you
will examine an unusually large bacterium, Bacillus megaterium. Since bacterial cells
are almost colourless, you need to stain them in order to see them.
1. Shake the Bacillus megaterium container to suspend the bacteria in the solution.
2. Place one small drop of the milky suspension on a clean microscope slide and
label it with your name. Spread the drop by gently rocking from side to side.
3. Place the slide on the side bench under the lamps and let the drop dry completely
to avoid the bacteria washing off the slide during subsequent procedures. While
the slide dries, proceed to “Comparison of size of eukaryotic and bacterial cells”.
4. When absolutely dry, add 1 drop of toluidine blue to the slide. After 5 minutes
rinse off the stain and then dry it completely under the lamps. Once dry, your
preparation is ready for examination by light microscopy.
5. Focus on the plane of the smear using the 10X objective. Then change to the 40X
objective. When the bacteria are in focus, swing the 40X objective out of the way
and place a drop of immersion oil on top of the bacterial smear. Now gently bring
the 100X objective into place. Only a slight adjustment of the fine focus knob
should be needed to view the Bacillus clearly.
6. Look at your bacterial cells and make a simple outline drawing (Figure 6).
54
Note: Bacterial cells are usually either rod-shaped or round, and may form clumps or
chains when growing in suspension.
Figure 6:
4. COMPARISON OF SIZE OF EUKARYOTIC AND BACTERIAL CELLS
In order to compare the sizes of your eukaryotic and bacterial cells, you need to
measure them carefully. You can measure Euglena or Spirogyra while your bacterial
smear is drying.
Euglena is a genus of green flagellates (protists that use a flagellum for locomotion).
They are green because they contain chlorophyll, and therefore photosynthesise.
However, if placed in the dark they can also feed by ingesting food particles.
Spirogyra is a green algae (eukaryote), composed of cells arranged in long

unbranched filaments. Each cell contains one or more long, green ribbon-like
chloroplasts that wind around the periphery of the elongated cells. As well as its
distinctive ribbon-shaped chloroplast(s), Spirogyra has a cell wall, and a large central
vacuole, and at its centre it has a nucleus.
1. Measure the length and width of about 10 mature Euglena / Spirogyra cells, and
from these measurements, calculate the average cell length and width. Record
your measurements and calculations.
55
2. As best as you can, estimate the average volume of a cell in the space below.
Assume the ‘width’ measurement is a the diameter.
3. Using the 100X oil immersion objective, make similar measurements on the
Bacillus cells. Be sure that you are only measuring the length of one bacterium,
not a group or chain of bacteria. Using the same assumptions as for Euglena /
Spirogyra, calculate the average cell volume below:
On completion of microscopic examination:
When finished with your microscope, before returning it to the cupboard, always:
o If appropriate, clean oil from the oil immersion lens and from other lenses too if
they have been contaminated with the oil
o Return the light intensity to the lowest setting and then switch off.
o Rotate the nosepiece back to the 4X position.
o Remove any slide from the stage.
o Dry any liquid from the stage.
o Secure the power cord.
PLEASE NOTE You must clean your lenses using the lens tissue provided. Never
use ordinary tissues as these can scratch lenses.
56
BABS Teaching Laboratory Practical 2: Cell Structure 2

BABS_RA_BABS1201_2

Follow demonstrators
Biological agent Infection instructions when handling
(Microorganisms, biological agents.
Rhodospirillium and Anabaena) PPCE (lab coats, closed in
Spills shoes & gloves as required).
Razor blades, glass Adhere to aseptic techniques.
slides/coverslips Notify demonstrator immediately
Cuts from broken glass of any spills or other incidents.
Carry slides/coverslips in
Razor blade cuts suitable containers and dispose
of any broken/used items
immediately in sharps
containers provided.
Proper handwashing with
antibacterial handwash before
leaving the laboratory.
Hazardous chemicals (nitroblue Eyes: Causes irritation. Personal Protection: Wear
tetrazolium salt) appropriate safety goggles,
Skin: Causes irritation. gloves and protective clothing.
Eyes: Immediately flush with
Ingestion: Harmful if swallowed plenty of water for at least 15
minutes. Skin: Immediately
Inhalation: Causes respiratory flush area with soap and water.
tract irritation. Label Hazard Warning:
Caution! May cause eye and
skin irritation. May cause
respiratory and digestive tract
irritation.
All used microfuge tubes should be placed in the biohazard bins. Used test tubes should be placed in
the appropriate container on the front bench of the lab. All solutions should be placed in the
requirements.
Signature:……………………………………………………………Date:……………………………
57
PRACTICAL 2
CELL STRUCTURE II
COMPARING CELLS USING THE LIGHT MICROSCOPE
CONTENTS
1. Staining mitochondria in eukaryotic cells

2. Staining nuclei in animal and plant cells
3. Cell walls, vacuoles & chloroplasts of eukaryotic cells
4. Other internal structures of eukaryotic cells
5. Staining bacterial cells
6. Staining of fixed cells

Revise the content covered in your lectures on Cells (using the lecture notes,
Mastering Biology resources, videos on Moodle and your textbook).
If you missed Practical 1, you must read through the notes and watch the video
on How to set up a microscope on Moodle.
OBJECTIVES
• To identify key differences between internal structures of bacterial and

eukaryotic cells using the light microscope
• To competently perform basic staining procedures and light microscopy of
different types of cells
• To identify an unknown cell type and describe your findings, including:
- identifying the type of cell (bacteria, eukaryote, plant or animal);
- describing the procedure used to identify the cells (such as the type of
stain);
- describing the characteristics of the cells that enabled you to identify
them (organelles, size, and structures).
58
1. STAINING MITOCHONDRIA IN EUKARYOTIC CELLS
Introduction:
Living cells come in a range of shapes, sizes and degrees of complexity. In this
practical you will perform staining - a procedure commonly used to assist in the
identification of cells. Different types of stains react with different kinds of molecules,
and so cell structures may or may not stain with different stains. We can therefow use
staining to identify cell structures and compartments.
There are two general ways of staining cells. They may be stained when they are
alive (‘vital stains’) or when they are dead. Cells are often chemically ‘fixed’ – a
technique that prevents decay and preserves important features of the cells. You will
use both types of stains in this class.
Mitochondria are not easily seen in living cells, but it is possible to increase their
visibility by staining them in a solution of pale yellow tetrazolium salt. This is a vital
stain which enters the cells and is reduced in the mitochondria to form an intense
coloured compound (purple or blue).
• Remember from the Risk Assessment that Tetrazolium salts are

hazardous!
• Ensure you wear safety glasses.
• Use the gloves provided, and when finished place them in the Scientific
Waste bins.
• NEVER leave gloves, used or unused, on the bench or in non-Scientific
Waste bins.
Procedure:
Make sure you set this up at the beginning of your class. The procedure needs to be
done carefully, and includes a 1 hour incubation. While the cells are staining, you can
proceed with other tasks.
1. Place about 10 drops of the tetrazolium solution into the container provided on
your bench. Immediately cover the container with foil to protect it from light, as
tetrazolium salts are sensitive to light and rapidly decay.
2. Cut several thin slices of surface tissue from the terminal centimetre of the broad
bean root tip with a razor blade, and place them immediately into the solution in
the container. Cover the container again and allow 1 hour for the reaction to take
place.
3. After one hour, mount a piece of tissue, using water and cover-slip, and examine
the thinnest part under the 10X and 40X and, if possible, the 100X oil immersion
objectives. It may help if you close down the condenser diaphragm to get higher
contrast. The mitochondria should appear as dark elongated or more or less
round structures, about the size of bacteria, throughout the cytoplasm.
59
Make a simple drawing of a cell and the mitochondria (Figure 1).
Figure 1:
Look at the electron micrographs of mitochondria available in the lab.
What structures can you see here that you cannot see under your microscope?
Why do you think you can’t see such structures in the cells you stained?
60
2. STAINING NUCLEI IN ANIMAL AND PLANT CELLS
In this procedure you will be using a stain, toluidine blue, that stains the nucleolus
purple (indicating the presence of RNA) and the nucleus pale blue (DNA).
Procedure:
1. Lightly scrape the inside of your cheek with the wooden stick provided. This
allows you to collect some of the so-called ‘epithelial cells’ that line many surfaces
of the body.
2. Mount the scrapings directly on a microscope slide, and add a drop of toluidine
blue solution. Leave 5 minutes for stain to work.
3. Cover with a coverslip and examine under 10X and 40X objectives.
Observe individual epithelial cells: what can you see?
4. Compare your cheek cells with the prepared slide of a corn root tip. In this
preparation, you will find many nuclei in various stages of division, but concentrate
on cells with nuclei that are not dividing, i.e. nuclei that have a clearly defined
circular outline and contain one or more nucleoli.
Can you see clear gaps between the cells in your corn root? What might this be?
Hint: what feature do plant cells have that animal cells don’t?
What are the major differences between the plant cells and your cheek cells (animal
cells)? What are the common features?
61
5. Draw two cells from both the cheek cell and the corn root preparations to show
their shape (Figure 2). Include their nucleus and any other internal structures that
you can see, making particular note of differences. Label your drawings and
include a scale.
Figure 2:
62
3. CELL WALLS, VACUOLES AND CHLOROPLASTS OF EUKARYOTIC

CELLS
Procedure:
You could not see details of the cell wall in your toluidine stained slides. Look at the
demonstration slide stained specifically to show the carbohydrate rich cell walls.
1. Plant cells often contain a central vacuole. Look at the electron micrographs of
vacuoles in plant cells. (What is a vacuole?)
Can you see central vacuoles in your corn root slides? Explain why this might be so.
2. With the forceps provided, carefully mount a young leaf of the water plant Egeria
in pond water, and examine with the 10X and 40X objectives.
Can you find chloroplasts?
What internal structures can you see in the chloroplasts?
How big are they?

63
3. Record your findings as a drawing with a scale (Figure 3).
Figure 3:
4. Leave your Egeria cells for a few moments to recover from the shock of being
removed from the plant, and look at it again.
What differences can you see?
5. Record your observations, and make a simple drawing of the main features that
you see (Figure 4).
Figure 4:
64
4. OTHER INTERNAL STRUCTURES OF EUKARYOTIC CELLS
There are other internal cell structures that are not visible down a light microscope.
Look at the electron micrographs that are available, and identify as many of the
features as you can. Record the structures that you recognise, and identify their
main function in Table 1.
Table 1:
Structure Function
65
4. STAINING BACTERIAL CELLS
Bacterial cells are generally smaller than eukaryotes, and have a less well defined
internal structure. This makes it difficult to see them well under light microscopy,
unless you use the high power (100X) oil immersion lens. Today you will look at two
different bacteria, and you will use several different stains.
Procedure:
Work in pairs and divide the work between you, but make sure you look at all slides.
Negative staining
Negative staining uses a stain that is excluded from the cells, so you have a dark
background with a light area highlighting each cell.
1. Mix a small drop of 4% nigrosine with a drop of Rhodospirillium suspension on a

clean microscope slide.
2. Using a clean cover slip, smear the suspension over the slide, and allow it to dry
completely under the lamp on the side bench.
3. Add one drop of immersion oil to the slide. This acts as a ‘mounting medium’,
allowing you to now to cover your specimen with a coverslip.
4. Look at your cells under 10X to focus, and then under 40X. When you have a
clear focus, add one drop of immersion oil on top of your coverslip, then examine
the slide under 100X. Make notes and/or drawings of what you see.
What shape are the bacterial cells?
Positive staining
Positive staining stains cells, leaving the background unstained. Toluidine blue is a
positive stain.
5. Put a drop of bacterial suspension on a slide, smear it as before, and allow it to

dry under the lamp.
6. Add one drop of toluidine blue solution on top of your smear, and leave it for 5
minutes on the bench.
7. Gently rinse the slide with distilled water, using the squeeze bottles provided. Be
careful not to squirt too hard, or you may wash the bacteria off your slide. Dry the
back of your slide with a tissue, then leave it under the lamp to dry completely.
8. When the slide is dry, place a drop of immersion oil on the smear as a mounting
medium, and cover with a coverslip.
66
9. Focus the bacteria clearly under the 40X objective, then add a drop of immersion
oil on top of the coverslip, and examine under the 100X objective.
What features can you see?
How does this stain compare with the nigrosine?
What shape are the bacteria?
10. Report your findings with a drawing, including a scale (Figure 5)
Figure 5:
67
5. STAINING FIXED CELLS
Using stains directly on cells can be useful, but often, much more detail is visible if
you fix your cells before staining. This is because fixing tends to make the membrane
more permeable, and allow the stain to better enter the cell. Many fixatives are used,
but a common one is ethanol. You are going to compare toluidine blue staining of
fixed and unfixed cells of the cyanobacterium, Anabaena.
Unfixed cells:
1. Mix one drop of toluidine blue with one drop of Anabaena suspension directly on a
slide. Cover it with a coverslip, and examine it under 40X.
Can you see the cell wall? (It should look like a pinkish fringe around the cell)
Describe:
Does the toluidine blue stain anything inside the cells?
Can you think of an explanation for this?
Fixed cells:
2. Place one drop of Anabaena suspension on a watchglass, and add one drop of
50% ethanol.
3. Mix well and leave for 2-3 minutes, then transfer one drop of this mixture to a
slide, and add one drop of toluidine blue. Mix and leave for 2-3 minutes to stain.
4. Transfer 1 drop of stained suspension to a new slide, cover it with a coverslip, and
examine it under 40X. If you need to move to 100X, add a drop of immersion oil
on top of the coverslip.
What are the main features you see?
What are the main differences between this slide and the unfixed cells?
68
Can you think of a reason for the differences?
5. Make a drawing of both fixed and unfixed cells. Label features that you can
identify, and indicate size with a scale (Figure 6)
Figure 6:
Write a brief explanation of the difference between the two slides.

69
SECTION 2:
EXPLORING CELL FUNCTION
PRACTICALS 3-4
Over the next two practical classes, you will perform accurate and repeatable
measurements of cell functions including:
• Osmosis and diffusion

• Photosynthesis and respiration
One of the crucial qualities expected of a scientist is to be able to accurately and

reproducibly measure a particular parameter of cell function in order to draw
conclusions and make new hypotheses, and it is upon this skill that these practicals
are focussed.
The aims for this section are:
• Calculate and report on parameters involved in diffusion through a semi-

permeable membrane.
• Investigate and report on the effects of osmosis on animal and plant cells.
• Use a pipettor to dispense a known volume, and make a dilution of a
concentrated solution.
• To investigate the effect of light intensity on the rate of photosynthesis
• To determine the rate of respiration in mung beans and the effects of different
metabolic inhibitors on that rate.

• Communication
• Teamwork, collaborative and management skills
70
BABS Teaching Laboratory Practical 3: Osmosis and

Diffusion
BABS_RA_BABS1201_4

Physical injury (glass capillary Cuts. Do not bend the capillary tube.
tube) Hold the tube close to the end
Breaking glass tube when being inserted through the
inserting into rubber bung. bung and take care to apply
force only along the axis of the
capillary tube.
Hazardous chemicals (Congo Warning! Causes eye irritation. Wear Personal protective
Red) May cause skin and respiratory equipment (gowns, safety
tract irritation. Possible risk of glasses, gloves and enclosed
harm to the unborn child. May shoes). Wash hands before
cause cancer in humans. May leaving the laboratory.
cause central nervous system
effects. Wear gloves and safety
Ingestion: May be harmful if glasses at all times when
swallowed. working with Congo Red.
Skin: May be harmful if
absorbed through skin. May Do not use personal items
cause skin irritation. such as mobile phones or
Eyes: May cause eye irritation. computers with gloves on.
Biological hazard (horse red Infection: contains animal blood Handle Material as potentially
blood cells) product. infectious.

All used gloves should be placed in the biohazard bins. Used test tubes should be placed in the
appropriate container on the front bench of the lab. All solutions should be placed in the

requirements.
Signature:……………………………………………………………Date:……………………………
71
PRACTICAL 3
CELL FUNCTION I
OSMOSIS AND DIFFUSION
CONTENTS
1. Osmosis Staining mitochondria in eukaryotic cells

2. Effect of osmosis on animal and plant cells

Revise the content covered in your lectures on Maintaining cell integrity and
Nutrient and ion transport (using the lecture notes, Mastering Biology resources,
videos on Moodle and your textbook).
OBJECTIVES
• Calculate and report on parameters involved in diffusion through a semi-

permeable membrane.
• Investigate and report on the effects of osmosis on animal and plant cells.
• Use a pipettor to dispense a known volume, and make a dilution of a
concentrated solution.
1. OSMOSIS
Introduction:
Movement of substances through cell membranes can, at one extreme, be entirely

dependent on physical factors (passive transport) or at the other extreme, may be
entirely dependent on specific transport mechanisms that require energy for their
function (active transport).
One of the most important factors influencing the passive movement of substances
through cell membranes is membrane permeability. All cells are enclosed by a
plasma membrane which is semipermeable. To be more accurate, the plasma
membrane is selectively or differentially permeable to various solutes. Osmosis is the
spontaneous net movement of water across such a semi-permeable membrane from
a region of low solute concentration to one with a high solute concentration, down a
solute concentration gradient. These descriptions all imply that the cell membrane is
much more permeable to water than it is to most solutes dissolved in the water.
The net movement of a solvent (substance, usually a liquid, in which other

substances are dissolved) is from the hypotonic (less-concentrated) to a hypertonic
(more-concentrated) solution. This results in a reduced difference between the
concentrations.
72
Experimental Procedure:
• Remember from the Risk Assessment that Congo red is hazardous!

• Ensure you wear safety glasses.
• Use the gloves provided, and when finished place them in the Scientific
Waste bins.
• NEVER leave gloves, used or unused, on the bench or in non-Scientific
Waste bins.
Work in pairs
In this part of the experiment, you will demonstrate osmosis using an artificial semi-
permeable membrane, and calculate the osmotic potential. The osmotic potential of a
solution that is separated from another solution by a semi-permeable membrane is a
measure of potential of the solution to suck water across the membrane.
1. Take a 10 cm length of dialysis (cellophane) tubing. Wet the ends of the tubing.
Insert a solid rubber bung into one end of the tubing and a perforated rubber bung
into the other end. Wrap one or two rubber bands tightly around each of the
rubber stoppers to make a leak-proof seal at each end of the dialysis tubing.
2. Over the sink, carefully fill the bag through the hole in one of the bungs with 3.5%
w/v Congo red solution (i.e. 3.5 gm Congo red in 100 Ml aqueous solution).
The molecular weight of Congo Red is approximately 700. What is the molarity of the
Congo Red solution?
3. Insert the capillary tube into the hole in the bung until the red solution appears at
the bottom of the tube above the bung. Do not bend the capillary tube. Hold the
tube close to the end being inserted through the bung and take care to apply force
only along the axis of the capillary tube. Wash the outside of the filled dialysis
tube with water to remove any spilled Congo red solution.
4. Examine the apparatus for leaks.
5. Support the capillary tube on a retort stand so that the capillary tube is vertical
and the dialysis bag is completely immersed in a beaker of distilled water, as
illustrated in Figure 1 on the following page.
73
Figure 1.
6. Note the level of the Congo red solution in the capillary tube.
7. Measure the level every 20 minutes for the next 2 hours and plot the results
against time on the blank graph provided as Figure 2 (don’t forget to give the
figure a title).
74
Figure 2:
75
8. Use Equation 1 below to calculate the osmotic pressure exerted by the congo red
solution under these circumstances. Show your calculations.
Equation 1: Dp = 1000 RT (Ci – Co )
Where:
p = osmotic pressure (N.m-2)
R = universal gas constant (8.3 J mol-1 K-1)
T = absolute temperature (Kelvin, note that 0 Kelvin = -273°C)
Ci = concentration inside bag (mol.L-1)
Co = concentration outside bag (mol.L-1)
9. Use Equation 2 below to calculate the height of water that can theoretically be
supported by this solution. Show your calculations.
Equation 2: P = r gh
Where:
r = density of water (1000 kg.m-3)
P = hydrostatic pressure (N. m-2)
g = acceleration of gravity (9.8 m.s-2)
h = height (m)
76
Given sufficient time, would the liquid column in the capillary tube reach this height?
Explain your answer:
10. Look at the demonstration using 2% methyl blue as the osmotic agent instead of
Congo red. The molecular weight of this molecule is almost the same as congo
red.
Can you think of a reason why Methyl blue readily escapes from the dialysis bag
while Congo red does not?
77
2. EFFECT OF OSMOSIS ON ANIMAL AND PLANT CELLS
Two solutions containing different solutes but having the same osmotic pressure are
called iso-osmotic. However, if these two solutions are separated by a membrane
they may not exert the same osmotic pressure across the membrane. This will
depend on the permeability of the membrane to each of the two solutes. When two
such solutions do exert the same osmotic pressure in a membrane system they are
described as being isotonic. Osmotic potential depends on solute concentration and
temperature whereas tonicity depends on solute concentration, temperature and the
relative permeability of the membrane to the solutes.
In the next exercise, the effect of osmotic gradients on animal and plant cells will be
demonstrated by lysis (bursting) of animal erythrocytes (red blood cells) and by
plasmolysis (cytoplasmic shrinkage) of plant cells.
Animal erythrocytes:
1. To measure the tonicity of animal erythrocytes (red blood cells) you will set up a
series of salt solutions of differing tonicities, and you will see whether the
erythrocytes lyse or not.
2. Set up a series of 10 labelled test tubes in a test tube rack.
3. Use the pipettor to dilute the stock 0.2 M (200 Mm) sodium chloride (NaCl)
provided with distilled water to make up the range of solutions given in Table 1.
Your tutor will demonstrate the correct use of the pipettor.
Table 1. Concentrations of NaCl
Tube Volume of Volume of dist. Final NaCl Result

NaCl (Ml) Water (Ml) conc. (Mm) (lysis or no lysis)
1 1.25 3.75 50
2 1.50 3.50 60
3 1.75 3.25 70
4 2.00 3.00 80
5 2.25 2.75 90
6 2.50 2.50 100

7 2.75 2.25 110
8 3.00 2.00 120
9 3.25 1.75 130

10 3.50 1.50 140
78
4. To each tube, add 0.1 ml sheep blood and shake well.
5. Let the tubes stand undisturbed in the rack for at least 1 hour to allow the non-
lysed cells to settle.
6. If the erythrocytes are not lysed, the tube will appear cloudy and red at the bottom
where the cells are, and clear at the top.
7. If the blood has lysed at all, the supernatant (above the cells) will begin to be
tinted red from the haemoglobin that has escaped from the burst cells.
8. With complete lysis, the tube will appear clear and red.
9. Place a piece of white paper behind the tubes, and identify which tubes show
each of the above features. Record your observation in the RESULTS column of
Table 1.
What is your estimate of the tonicity of the erythrocytes? Explain your answer:
Solute permeability
In this experiment, you will investigate the effect of solute permeability into
erythrocytes on the outcome of the lysis process, remembering that unless the solute
can penetrate the erythrocyte membrane, osmosis cannot occur. All the solutions
you will use are 330 Mm. A range of different solutions, including sucrose, glucose,
urea, glycerol and ethyl alcohol are provided.
Decide what factors might affect the permeability of different solutes into
erythrocytes. Explain your reasoning:
10. Choose two solutions from those available, making sure you choose one that you
think will easily penetrate the cells, and one which will not. Make sure that at least
one person within your bench group will be testing every solution.
11. Place 2 Ml of each of your solutions into separate small test tubes. Add 2 drops of
blood to each tube and quickly stir.
79
12. Using a stop watch if necessary, note the time taken for complete lysis of the
erythrocytes. Keep checking your tubes at 1 minute intervals for the first 10
minutes, then 5 minute intervals for one hour if necessary.
13. Record the time taken for lysis in each of your tubes. Consult with the other
members of your bench group, and complete the table of the time taken for lysis
upon exposure to each solution (Table 2).
Table 2: Estimation of induced lysis of erythrocytes
Solution Time until complete lysis of erythrocytes
Were the erythrocytes affected by the different solutions in the ways that you
predicted? If this was not the case, can you suggest reasons for this?
80
Estimation of osmotic concentration of plant cells:
When plant cells are immersed in a hypotonic solution, the large vacuoles of the cells
swell until the positive hydrostatic pressure has increased to balance the negative
osmotic potential.
Why doesn’t the cell burst like an animal cell?
The average osmotic concentration of the intracellular fluid of the population of plant
cells can be estimated using the phenomenon of plasmolysis.
Plasmolysis occurs when the osmotic potential gradient is reversed by placing cells in
a hypertonic solution. Water then diffuses out of the vacuole into the external
solution. Incipient plasmolysis describes the condition when a solution removes
sufficient water to cause the protoplast to detach from the cell wall.
The concentration that causes plasmolysis in 50% of the cells can be estimated by
placing pieces of plant tissue into a graded series of solutions. This concentration is
isotonic with the vacuolar contents of an average cell in the tissue.
You should work as a bench group for this experiment. Each student should perform
counts on at least two tubes.
Students are advised to put gloves on when handling Rhoeo because the plant can
be an irritant.
Procedure:
1. Cut 9 thin slices from the purple epidermis on the underside of the Rhoeo leaf.
Note: any slice that has numerous green photosynthetic cells attached to its
under-surface is too thick. Immerse the slices in distilled water as they are cut
2. Set up a series of 8-10 labelled specimen tubes.
3. You will now use the pipettor to dilute a 0.5 M (500 Mm) NaCl solution with
distilled water to a range of concentrations from 500 Mm down. Make sure you
cover the range well so you can narrow down the concentration that is isotonic
with the plant vacuole.
4. You need a total volume of 10 Ml in each tube, so use the table below to help you
calculate the relative volumes of NaCl and water you need for each concentration.
For example, if you wanted to test NaCl at 500 Mm, you would add 10 Ml NaCl
solution and 0 Ml distilled water. If you wanted to test 250 Mm, you would add 5
Ml NaCl solution plus 5 Ml distilled water. Complete Table 3, to indicate the range
of concentrations you will test.
81
Table 3: Concentrations of NaCl for testing plasmolysis
Tube Volume of NaCl Volume of distilled Final NaCl concentration

(mL) water (mL) (mM)
Show your table to your demonstrator. While there is no one correct answer for the
appropriate concentrations of NaCl to use, your tutor will review your calculations for
the dilutions.
5. Before placing any pieces of plant epidermis into the tubes, mount one slice in
distilled water on a microscope slide with the cuticle uppermost, and cover with a
cover-slip.
6. Select two tubes from your series, one from the highest half of the dilutions series,
one from the lower half, e.g. you might choose tubes 1 and 5, or 2 and 6 etc.
7. At 3 minute intervals, totally immerse one of the slices of epidermis in one of your
tubes, and leave for 20 minutes.
8. After 20 minutes, remove each piece, and mount it in the solution in which it was
soaking on a microscope slide with the cuticle uppermost, and cover it with a
cover-slip.
9. Immediately examine at least 50 cells for plasmolysis. Any cell showing visible
separation of the purple protoplast from the cell wall should be counted as
plasmolysed.
10. Record the total number of cells you count, and the number of these that are
plasmolysed. From this, calculate the percent plasmolysed at each NaCl
concentration.
82
Obtain the results from other members of your group, and record all in Table 4.
Table 4: Results
Tube NaCl Total no. No. of cells % cells

concentration cells plasmolysed plasmolysed
(mM) counted
83
Plot the % plasmolysis versus NaCl concentration as Figure 3 below.
Figure 3:
84
What concentration do you estimate to be isotonic with your plant cells?
Would the intracellular fluid of Rhoeo be isotonic, hypertonic or hypotonic with

respect to the sheep erythrocytes you investigated earlier?
What occupies the space between the plasmolysed protoplast and the cell wall of
the Rhoeo cells?
HOMEWORK: MASTERING BIOLOGY
Before your next laboratory class there are three Mastering Biology tutorial activities
for you to complete. The activities will also help you prepare for your Mastering
Biology Quiz 3 Photosynthesis, which is an assessable part of the course.
Work through the following three BioFlix tutorials:
ITEM MEDIAN
TYPE TITLE TIME
Photosynthesis (1 of 3): Inputs, Outputs, and Chloroplast Structure
Tutorial 14 min
(BioFlix tutorial)
Tutorial Photosynthesis (2 of 3): The Light Reactions (BioFlix tutorial) 11 min
Tutorial Photosynthesis (3 of 3): The Calvin Cycle (BioFlix tutorial) 10 min
85
BABS Teaching Laboratory Practical 4: Photosynthesis and

Respiration
BABS_RA_BABS1201_5

General See below At all times follow
demonstrators instructions when
handling all biological
substances, chemicals and
equipment items. Notify
demonstrator immediately of any
spills or other incidents. NO
eating drinking or smoking in
lab.
PPE (lab coats, closed in shoes
& gloves as required), Dispose
of all sharps in the sharps
containers provided on your
bench. Proper handwashing
before leaving the laboratory.
Physical injury (plastic capillary Cuts. Do not bend the capillary tube.
tube) Hold the tube close to the end
Breaking tube when inserting being inserted through the
into rubber bung. bung and take care to apply
force only along the axis of the
capillary tube.
Hazardous chemicals (soda Warning! Soda lime is a strong Wear Personal protective
lime) alkali. Do not get in on skin or equipment (gowns, gloves and
clothing. If you do, wash the enclosed shoes). Wash hands
affected area for several before leaving the laboratory.
minutes with running water.
Wear gloves at all times.
requirements.
Signature:……………………………………………………………Date:……………………………
86
PRACTICAL 4
CELL FUNCTION II
PHOTOSYNTHESIS AND RESPIRATION
CONTENTS
1. Photosynthesis
1a. Rate of photosynthesis and light intensity in a whole plant
1b. Structure of a chloroplast
1c. The Hill reaction
2. Respiration

Complete the following three Mastering Biology tutorial activities. The activities
will also help you prepare for your Mastering Biology Quiz 3 Photosynthesis,
which is an assessable part of the course.
ITEM MEDIAN
TYPE TITLE TIME
Photosynthesis (1 of 3): Inputs, Outputs, and Chloroplast Structure
Tutorial 14 min
(BioFlix tutorial)
Tutorial Photosynthesis (2 of 3): The Light Reactions (BioFlix tutorial) 11 min
Tutorial Photosynthesis (3 of 3): The Calvin Cycle (BioFlix tutorial) 10 min
OBJECTIVES
• To investigate the effect of light intensity on the rate of photosynthesis

• To determine the rate of respiration in mung beans and the effects of different
metabolic inhibitors on that rate.
87
1. PHOTOSYNTHESIS
Introduction:
Photosynthesis is frequently defined as the process by which green plants
manufacture carbohydrates from carbon dioxide and water, using radiation from the
sun as a source of energy. The overall process is summarised by the equation:
carbon dioxide + water glucose + oxygen
6CO2 + 6H2O C6H12O6 + 6O2
Photosynthesis is not a single one-step process as this equation implies, but a

complex series of chemical reactions. The overall process is divided into two quite
separate parts.
The so-called light reactions are a series of photochemical reactions that take place
on the thylakoid membranes of the chloroplast. These reactions are also called the
Hill reactions. In these reactions:
o The energy provided by light splits a water molecule

o Gaseous oxygen is liberated as a result
o The energy from the light is trapped in the short-term chemical
intermediaries ATP and NADPH
The so-called dark reactions are reactions in which carbohydrates are made from
carbon dioxide by using the reducing power of the ATP and NADPH generated in the
light reactions. Since production of carbohydrates can occur with or without light, it is
perhaps misleading to call it the dark reaction, and the process is better termed the
Calvin cycle. Only the light reactions are unique to photosynthesis. You will look at
this part of the process today.
1a RATE OF PHOTOSYNTHESIS & LIGHT INTENSITY IN A WHOLE PLANT
Demonstration:
This experiment using the aquatic plant Egeria densa has been set up as a
demonstration. The rate of photosynthesis at different light intensities was measured
by the rate of oxygen production, as indicated by the rate of bubbling. Other factors
that might affect the photosynthetic rate were kept constant. The data are set out
with the demonstration. These light measurements were made on the axis of the
lamp, in the centre of the beam. They do not follow the inverse square law because
the lamp and reflector are not a point source over these distances.
88
Why is the relationship between photosynthetic rate and light intensity curvilinear
with a tendency to saturate at higher light intensities?
89
1b STRUCTURE OF A CHLOROPLAST
Examine the electron micrograph of a chloroplast.
Identify and label the following components of a chloroplast ( Figure 1).
• The inner and outer membranes

• The thylakoid membrane stacks (grana)
• The stroma
• the location of the Hill reaction (light reactions) and the Calvin cycle (dark
reactions).
Figure 1: Chloroplast.
1c. THE HILL REACTION
In 1939, Robin Hill of Cambridge University found that suspensions of chloroplasts

isolated from leaf cells yielded oxygen when illuminated in the presence of an
electron acceptor, that is, an oxidising agent. Hill demonstrated the essential
features of the light reactions. These reactions are summarised in Figure 2.
Figure 2. Summary of the light reactions.

90
Since the oxidising agent used by plants in intact chloroplasts is NADP+, the light
reaction can be written as:
2H2O + 3ADP + 3P + 2NADP+® O2 + 2NADPH + 3ATP + 2H+
Hill used an artificial oxidising agent, ferric cyanide. Modern versions of the reaction
use an oxidising agent called dichlorophenolindophenol (DPIP for short) in place of
NADP. So the Hill reaction can be written as:
light
2H2O + 2DPIP* ® 2DPIPH2** + O2 (in the presence of chloroplasts)
*Oxidised DPIP is blue

**Reduced DPIP is colourless.
Therefore, the rate of disappearance of the blue DPIP indicates the rate of the
Hill reaction.
No ATP is made in the Hill reaction because the method of preparation partially
ruptures the chloroplast membranes. Thus, the gradient of H+ concentration, which
drives ATP synthesis, cannot form.
The Hill reaction was the first demonstration of an in vitro (literally, in glass, that is a
test-tube) reaction similar to the photosynthetic activity of the chloroplasts during in
vivo (literally, in life) photosynthesis.
Aim:
The aim of this experiment is to demonstrate the transfer of electrons from

chlorophyll a to a suitable electron acceptor and the subsequent replacement of
those electrons from water molecules so releasing O2.
Preparing the chloroplasts:
1. Work in groups of 3. Take 5 g of spinach leaf. Remove the main vein and grind up
the leaf tissue with a 1/4 teaspoon of sand and 3 mL of buffer-sucrose solution.
Grind thoroughly keeping the mortar and pestle on ice. When the visible lumps
have disintegrated, add a further 11 mL of buffer to the homogenate.
2. Put a 100 mL beaker in an ice bucket to act as a receptacle and strain the
homogenate through two layers of damp cheese-cloth into the chilled beaker.
Squeeze the cheese-cloth out to make sure that all liquid is extracted into the
beaker.
3. Take a larger test tube and mark it at a level equivalent to 30 mL volume. Pour
the mixture from the beaker into the large test tube and add buffer to make the
volume up to the 30 mL mark. Keep the mixture on ice. Stir the mixture before
taking an aliquot for the experiment.
91
Trial run:
1. Wrap a thin sheet of foil around each of two test tubes. Leave them in a test tube
rack. Label the tubes A and B. To A add 6 mL of buffered sucrose solution and
0.5 mL of 2,6 dichlorophenolindophenol (DPIP, strength 0.4 mmol.L-1). To tube B
add 6.5 mL of buffered sucrose solution.
2. Half-fill a beaker to act as a water bath. Place the test tube holder in the beaker,
with 2 empty tubes (the rubber rings are for the bottom of the tubes, so they stay
upright).
3. Direct a 240 V 60 W bench lamp onto the tubes at about 10 cm distance from
them (that is, 10 cm from the rim of the lamp holder to the test tubes), but keep
the light turned off. Check that your light is in a direct line with the tubes.
4. Add 0.5 mL of your chloroplast suspension to each of tubes A & B and stir the
mixture. Quickly remove the foil from tubes A and B. Remove the empty tubes
from the holder in the H2O bath and replace with tubes A and B.
5. Turn on the light. Start the timer and time the disappearance of the blue colour
from the tube containing DPIP (e.g. when the tube containing DPIP is the same
green colour as the control tube).
Which reaction leads to this change in colour?
Effect of light intensity:
Repeat the above experiment with the bench lamp at 15, 20, 40 and 60 cm from the
test tubes.
From the standard curve provided on the side bench, calculate the light intensities at
each distance. Enter all your results in the table below. The constant initial
concentration of DPIP has been entered for you.
Table 1.
Distance (cm) 10 15 20 40 60
Light intensity
A. Initial DPIP (nmol) 200 200 200 200 200
B. time for decolourisation (sec)
C. Rate of breakdown (A/B)

92
Express your results as a graph (Figure 3). Make sure your graph is fully labelled and
accurately represents the data in the table.
What can you conclude from this experiment?
What is the role of tube B? Is it effective in this role? If not, what would you suggest
in its place?
93
Figure 3:
94
2. RESPIRATION
Introduction:
In its broadest meaning, respiration means the release of energy from complex
organic molecules built up during the process of photosynthesis. The overall process
can be summarised as:
Thus, respiration reverses the action of photosynthesis by liberating the chemical

energy stored in the glucose molecule. However, respiration is not simply a reversal
of the reaction sequence of photosynthesis.
There are several ways in which we can demonstrate that respiration is

occurring in an organism:
• by measuring the energy given off in the form of heat,
• by measuring the amount of glucose used,
• by determining the amount of oxygen consumed,
• by measuring the amount of carbon dioxide given off.
Today you will measure respiration in beans by measuring oxygen consumption.
The experiment will be performed with a respirometer.Changes in the volume of gas

in the respirometer are shown by the movement of coloured fluid in a plastic tube
connected to a container.
Procedure:
Work in groups of 3.
• Soda lime is a strong alkali. Do not get in on skin or clothing.

• Ensure you wear safety glasses and gloves.
• If some spills on your skin or clothing, tell your demonstrator immediately
and wash the affected area for several minutes with running water.
95
1. Fill a test tube with germinated mung beans.
2. Put soda lime in the small wire basket and place it in the test tube, making sure
that it is not touching the beans.
3. Using the Figures 4 and 5 as a guide, construct your respirometer as follows:
Figure 4: Respirometer design.
Figure 5: Respirometer design.

96
4. Dampen the sides of the rubber bung with water and insert it with its plastic tube
firmly into the test tube.
5. Attach the pinch clamp to the rubber tubing, but do not clamp it yet. A millimetre
scale is firmly attached to the plastic tube.
6. Set up the respirometer in a horizontal position on the stand.
7. Affix the flat-bottomed tube containing the dye solution to the other end of the
plastic tubing so that the end of the plastic tubing is about one centimetre from the
bottom of the tube containing the dye.
8. Keep your respirometer away from heat sources, as it is very sensitive to heat.
9. Allow your experiment to equilibrate for about 5 minutes, and then tighten the
clamp.
10. Wait several minutes until the end of the dye column reaches the millimetre scale.
Take the initial reading for your experiment.
11. Over the next 45 minutes, take readings of the location of the liquid at 5 minute
intervals. Compare your results with the demonstration of sterilsed beans set up
in the laboratory.
12. At the end of your experiment, the dye column can be returned to the flat-
bottomed reservoir container by opening the pinch clamp and tilting the plastic
tube. Blow any droplets of dye solution remaining in the plastic tube onto a piece
of paper towel using compressed air from the tap at the front of the laboratory.
13. Analyse your results as follows:
14. The internal diameter of the plastic tubing is 3.0 mm. Use the formula for the
volume of a cylinder to calculate the volume of gas consumed in the tube at each
time point. Record your results in Table 5.
15. Plot a graph (Figure 6) of your experimental results on the graph provided over
the page, showing the cumulative volume of gas consumed in the tube at three
minute intervals. Make sure that your graph is well labelled and that the data
correspond to those in your table.
16. Compare your results with those of other groups.

97
How reproducible are your results? How can you evaluate this?
Why is it necessary to put soda lime into the respirometer?
What is the purpose of the sterilzed mung beans? Can you think of an alternative
way of doing this?
Was there a difference in the oxygen consumption of the fresh and sterilised mung
beans? If so, can you explain this?
Did you observe water vapour within the respirometer? Where may this water have
come from?
98
Table 2.
Time (min) Height of liquid (mm) Volume of gas consumed (ml)

0 0 0
5
10
15
20
25
30
35
40
45
99
Figure 6:
100
SECTION 3:
EXPLORING GENES
PRACTICALS 5 - 6
Your mission in this section is to explore:
• The roles of genes and DNA in inheritance.
• The mechanisms by which DNA is passed from cell to cell when they divide.
• The use of molecular biology in disease diagnosis.
The third and final sequence of practical classes involves two labs exploring aspects
of cell division, genetic inheritance, and molecular biology related to the concepts that
will be discussed in lectures.
With the publishing of the human genome (all the genes in a human), and of multiple
genomes of other living organisms including mice, dogs, horses, many plants, many
bacteria and viruses, and many protists, modern genetics is one of the most
important basic sciences supporting modern biological research. It is on some of the
important concepts underlying genetics that this section is focussed.
The goals for this sequence are:
• Describe human karyotyping and its role in ascertaining sex and detecting
chromosomal abnormality.
• List and explain the stages in mitosis and meiosis.
• Compare and contrast meiosis and mitosis.
• List the reagents needed in a PCR and explain their purpose.
• Interpret the results of a PCR experiment, and construct a pedigree from those
results.

• Teamwork, collaborative and management skills
101
BABS Teaching Laboratory Practical 5: Genes I: Mitosis

and Cell Division
BABS_RA_BABS1201_7

demonstrators instructions when
handling all biological
demonstrator immediately of any
spills or other incidents.
Physical injury (razor blades, Cuts Do not walk around laboratory

needles) with exposed sharps. Dispose
of all used blades in the sharps
bins provided on your bench.
Hazardous chemicals (45% Do not get in on skin or clothing. Wear Personal protective
acetic acid mounting medium, If you do, wash the affected equipment (gowns, gloves and
70% ethanol) area for several minutes with enclosed shoes). Wash hands
running water. before leaving the laboratory.
Wear safety glasses when
working with concentrated acid.
Wear gloves at all times.

appropriate liquid waste containers. Used razor blades, slides and cover slips should be placed in
approved biohazard sharps containers.

requirements.
Signature:……………………………………………………………Date:……………………………
102
PRACTICAL 5
GENES I
MITOSIS AND MEIOSIS
CONTENTS
1. Observing karyotypes
2. Mitosis in the onion root tip
3. Meiosis
4. Setting up a PCR

Complete the following three Mastering Biology tutorial activities. The activities
will also help you prepare for your Mastering Biology Quiz 4, which is an
assessable part of the course.
ITEM MEDIAN
TITLE
TYPE TIME
Meiosis (1 of 3): Genes, Chromosomes, and Sexual
Tutorial 13 min
Reproduction (BioFlix tutorial)
Tutorial Meiosis (2 of 3): The Mechanism (BioFlix tutorial) 10 min
Coaching
Video Tutor Session Quiz: Mitosis vs. Meiosis 5 min
Activities
OBJECTIVES
• Describe human karyotyping and its role in ascertaining sex and detecting
chromosomal abnormality.
• List and explain the stages in mitosis and meiosis.
• Compare and contrast meiosis and mitosis.
• List the reagents needed in a PCR and explain their purpose.
results.
• Define and explain Mendel's law of segregation (the first law).
• Apply Mendel's first law to a simple cross between two heterozygous
individuals.
• Demonstrate the alternative possible arrangements of homologous chromosomes
during metaphase I of meiosis.
• Relate the arrangement of homologous chromosomes in metaphase I to the
number of types of genetically different gametes that can be produced.
• Define & explain Mendel's law of independent assortment (the second law).
• Verify that the law of independent assortment holds true for alleles in a dihybrid
cross between two heterozygous individuals.
• Observe genomic DNA and its properties.
103
INTRODUCTION
The production of new cells continues throughout the life of any multicellular plant or
animal. Unless there is some mishap, each cell divides to produce two exact genetic
replicas of itself. This is the result of a process called mitosis, the division of the
chromosomes. The chromosomes are located in the nucleus, and they contain the
DNA, which carries the genetic information. The genes controlling a specific
characteristic, for example, eye colour, are always at the same place (“locus”) on a
specific chromosome.
Understanding mitosis (and meiosis) is important for understanding how genetic

information is passed from a cell to its daughter cells.
We will follow the behaviour of these chromosomes through a complete cycle of cell
division. Although it is a continuous process, mitosis is divided into stages for
convenience. These stages, which can be recognised down the microscope, are
named as follows: prophase, metaphase, anaphase, telophase.
Successive mitotic divisions alternate with a much longer interphase. Diagrams and
photographs of each stage are placed around the laboratory. For more detail on each
of these phases, see the textbook.
Figure 1: The cell cycle. G1 is the first growth phase, and G2 is the second
growth phase.
104
Human karyotype
A somatic human cell is diploid and usually contains 46 chromosomes, consisting of
23 homologous pairs. One of the homologous pairs are the sex chromosomes (XX in
females or XY in males). The non-sex chromosomes are called autosomes. The
karyotype of a species describes the chromosome complement of an organism in
terms of chromosome number and length, centromere position and any other
characteristics such as banding patterns seen with certain staining methods.
Many human hereditary defects caused by chromosomal abnormalities can be

identified by examining human chromosomes from cells that have been arrested in
metaphase of mitosis – a stage when chromosomes are very short and compact.
Leukocytes (white blood cells) or fetal cells obtained by amniocentesis or chorionic
villus sampling are often used for diagnosis.
The cells are cultured (to increase their number), treated with a chemical that disrupts
the mitotic spindle (to stop mitosis), and placed in a hypotonic salt solution (to swell
their nuclei). (Note: the mitotic spindle is a structure made of microtubules, which
coordinates the movement of chromosomes during cell division).The mixture is then
centrifuged (to increase the concentration of cells) and transferred to a glass slide. As
a drop of the cell suspension hits the slide, the nuclei break open and the
chromosomes spread apart; usually chromosomes from a single cell remain in an
identifiable group. The cells are then stained using procedures that result in banded
chromosomes.
In the early days of studying the human karyotype, it was hard to tell individual
chromosomes apart. So they were classified into seven major groups, A through G.
These groups were based on their length and the position of the centromere (the
constricted point on the chromosome). The groups were:
Group A Chromosomes 1-3 Group B Chromosomes 4 and 5

Group C Chromosomes 6-12 Group D Chromosomes 13-15
Group E Chromosomes 16-18 Group F Chromosomes 19 and 20
Group G Chromosomes 21 and 22 Sex chromosomes X and Y
Eventually, scientists could tell individual chromosomes apart thanks to coloured

bands that were visible after staining (“painted chromosomes”).
Karyotype analysis involves a number of steps that enable visualisation of an

individual’s chromosomes. First, cells from the individual (typically peripheral blood
lymphocytes) are isolated and cultured in vitro. Cell division is then arrested using
colcemid (which inhibits formation of the mitotic spindle); the cells are treated with
hypotonic solution (to swell them and separate the chromosomes); a fixative is added
(to kill and permeabilise the cells) and the chromosomes are stained with a
chromatin-staining dye (e.g. Giemsa). Finally, the cells are ‘squashed’ on microscope
slides and cells with clearly visible chromosomes (generally at metaphase in the cell
cycle) are identified under the microscope. Homologous chromosomes have
distinctive lengths, centromere positions and staining patterns, and these features
are used to identify and organise the chromosomes into a karyotype (see Figure 2).
By convention, the karyotype is constructed by pairing the autosomes and arranging
them in order of size (from largest to smallest) and centromere position
(metacentric→submetacentric→acrocentric→telocentric; see Figures 2 and 3). Image
analysis software is often used to build and analyse the karyotype.
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1. OBSERVING KARYOTYPES
Prepared slides
Examine slides of a metaphase preparation from white blood cells provided in the
class. Locate a cell in which the chromosomes seem to be well spread out under the
40X objective, and then transfer to the 100X oil immersion lens. See if you can
determine (a) what sex the donor was and (b) whether there is an abnormal number
of chromosomes. (It may not be possible to determine this, but try).
Abnormalities in a karyotype
Any abnormalities in the individual’s karyotype (or idiogram) may be identified by

comparing the karyotype with a normal reference karyotype. This enables the rapid
detection of abnormal numbers of chromosomes (e.g. trisomy 21) and large changes
in chromosome structure (e.g. deletions, inversions and translocations). However,
small (<1Mbp) abnormalities are generally not visible and must be identified using
molecular techniques.
Figure 2: Karyotype of a human male using Giemsa staining

106
chromatids
centromeres 1. Metacentric
2. Submetacentric
3. Acrocentric
4. Telocentric
1 2 3 4
Figure 3: Centromere locations
Observing HeLa cell karyotypes
Your aim is to prepare and analyse metaphase chromosome spreads (Figure 3).
You will be provided with a suspension of fixed cancer (HeLa) cells that have been
commercially prepared for karyotyping. The HeLa cell line is widely used in cancer
and cell biology research and has an interesting history: it was isolated without
consent from an aggressive cervical carcinoma in the patient Henrietta Lacks in the
1950s, and became widely used in research as it is relatively easy to maintain in
culture. (Why do you think this cell line is easy to culture?). You will stain the
prepared cells and mount them.
Figure 3: HeLa cell metaphase chromosome spread

107
Procedure:
Work in pairs.
1. Place a microscope slide at a 45° angle on your bench.
2. Adjust a P1000 micropipette to 250 μl and attach a blue tip.
3. Gently resuspend the cells in the tube provided by slowly pipetting up and down.
4. Remove 250 μl of suspension from the tube. Hold the pipette 60 cm above the
microscope slide. Allow one drop of cell suspension to “splat” onto the slide about
2 cm from the upper end and tumble down the slide. Carefully apply 6-8 more
drops from various heights, one drop at a time, onto the same region of the slide.
It is important to release the cell suspension one drop at a time. Do not expel all
of your cell suspension in one squirt, or you will obtain poor results. Gently blow
across the slide (and away from yourself and others) for 2-3 seconds. This drying
will help “spread” the chromosomes.
5. Allow the cells to AIR DRY COMPLETELY.
6. Dip the slide into the tube containing STAIN #1 for 1 second only. Repeat twice.
7. Drain off excess stain, wipe bottom of slide with paper towel (to minimise
carryover) and dip the slide into STAIN #2 for 1 second only. Remove slide and
repeat dipping twice.
8. Remove slide from stain and thoroughly rinse by dipping several times in 50ml
tubes filled with distilled water.
9. Allow slide to AIR DRY COMPLETELY. Blowing may help speed up the drying
process. Incomplete drying will result in very poor resolution.
10. Place a #1 coverslip over the slide and secure in place by painting around the
edges of the coverslip with nail varnish. Allow to dry. You may wish to place
coverslips side-by-side so as to allow viewing of the entire microscope slide.
11. Observe your slide using the 10X objective. Scan the spread for cells which
appear to have ruptured and released their chromosomes and then shift to 40X
objective to examine your spread more carefully. An ideal chromosome spread
will contain distinct non-overlapping chromosomes with clearly visible sister
chromatids (see Figure 3).
12. Count the number of chromosomes in 2-3 cells and answer these questions:
108
How many chromosomes would you expect to see in normal cells?
Do the HeLa cells contain a constant number of chromosomes? Explain your

observations in terms of the differences between normal and cancer cells.
How could you reliably identify chromosomal abnormalities (if present) from your
metaphase spreads?
Suggested reading
Two books that give fascinating accounts of the history of HeLa cells:
Skloot, R. (2010) The Immortal Life of Henrietta Lacks.

Crown Publishers, New York.
Gold, M. (1986) A Conspiracy of Cells. SUNY Press.

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2. MITOSIS IN THE ONION ROOT TIP
In today’s lab you will be given a root tip of an onion plant. It was fixed (killed) by a
mixture of acetic acid and alcohol and soaked for a short time in 70% ethanol to clear
the cytoplasm of oil droplets and other material that might make the chromosomes
difficult to see. It was then stained in aceto-carmine and stored in 45% acetic acid.
This procedure destroyed the spindles and stained the chromosomes red.
Preparing a root tip squash:
This technique will be demonstrated in a video.
1. Place a root tip on a microscope slide and cover it with a drop of 45% acetic acid,
the mounting medium.
2. If the root tip is thick, split it lengthwise. Keep one half on the present slide and
transfer the other half to a drop of 45% acetic acid on a second slide. Thus, two
slides can be made from one tip.
3. Hold the cut end of the root with a pair of forceps and cut off about 1 to 2 mm of
the pointed tip, the deeply stained meristem, with a sharp razor blade. Discard
the remainder of the root.
4. Cut the 1 to 2 mm of the tip remaining on your slide into 3 or 4 pieces. Spread
these in the drop of acetic acid containing gum chloral to prevent drying out.
5. Cover the tip with a cover-slip. Avoid all movement of the cover slip from now on.
6. Hold the edge of the cover-slip with your fingers and tap the surface firmly with
the blunt end of a pencil, dissecting needle or forceps to spread the cells - the red
blobs of tissue should spread into pink smears.
7. Place the slide, cover-slip down, on a tissue then fold the tissue over the slide.
Hold both ends of the slide firmly with one hand, and use the thumb of the other
hand to press on the centre of the slide. It helps squash the cells if you roll your
thumb slightly as long as you do not move the slide about.
8. Examine the whole preparation under the lowest power of the microscope and
identify interesting cells.
What makes a cell interesting? Can you see the chromosomes, and can you identify
cells at different stages of the cell cycle?
110
If the cells are not in a single layer, repeat the previous step. Switch to 40X objective
and study the cell in detail. Return to low power when searching for other stages.
This will speed your work immensely. Remember that you need to continually adjust
the focus when using high power.
In the spaces below, draw a cell at metaphase (Figure 2) and a cell at anaphase
(Figure 3). Write captions for your drawings and label them fully, including the
following where appropriate: centromere, sister chromatids, daughter chromosomes.
Sister chromatids are the two copies of a chromosome produced through DNA
replication during S phase. They are attached to each other at the centromere until
they separate during anaphase.
Figure 2:
Figure 3:
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3. MEIOSIS
Introduction:
Sexual reproduction allows the genes of two individuals to combine and provides the
variability upon which evolution can work. In sexually reproducing organisms, the
production of sex cells, or gametes, requires that each parent's chromosomes be
reduced to half the normal number.
This halving of the parent's chromosome number from the diploid, or 2n, number to
the haploid, or n, number is the result of meiosis. Combining two haploid (n) gametes
during fertilization then restores the chromosome number to the number that is
characteristic of the diploid (2n) organism (Figure 4).
diploid parent haploid gamete

(2n) (n)
meiosis
new diploid
fertilisation individual
(2n)
diploid parent haploid gamete

(2n) (n)
meiosis
Figure 4: Meiosis in animals
Meiosis consists of two nuclear divisions (meiosis I and meiosis II) and results in the
production of four daughter nuclei, each of which contains only half the number of
chromosomes (and half the amount of DNA) characteristic of the parent (Figure 5).
Define following terms:
diploid
haploid
homologous
chromosomes
locus
heterozygous
homozygous
dominant
recessive
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Diploid parent
nucleus with two
chromosomes
DNA duplicates
Each
chromosome
consists of two
chromatids
Meiosis 1
First nuclear
division
Daughter cells
contain half the
number of Chromosomes
chromosomes separate
characteristic of
parent cell
Meiosis II
Second nuclear
division
Haploid
daughter Chromatids
cells separate
Figure 5: Overview of meiosis. In this example, diploids have 2n=2

chromosomes.
During meiotic reduction of the chromosome the chromosomes are not just divided
into two sets at random. In diploid organisms, chromosomes occur in matched pairs
called homologous chromosomes. These are identical in size, shape, location of
their centromeres, and types of genes present.
One member of each homologous pair is contributed by the male parent and one is
contributed by the female parent during sexual reproduction. Meiosis provides a
precise mechanism for separating these homologous chromosomes so that
daughter cells always carry one member, or homologue, of each chromosome pair.
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How many cells form during the process of meiosis?
Are the cells formed in meiosis haploid (n) or diploid (2n)?
If the same set of chromosomes shown above were to undergo mitosis, would the
resulting cells be haploid or diploid?
List three major differences between meiosis and mitosis:

1.
2.
3.
3. SETTING UP A PCR
The aim of this experiment is to introduce you to some molecular techniques that are
used in medical diagnostics.
Perhaps the most important of these is PCR, which allows the amplification of
specific gene sequences in any DNA sample, such as those collected for forensic
and diagnostic screening. You will use this technique to screen some DNA samples
for deletions in the Duchenne’s Muscular Dystrophy gene and determine a family
pedigree for this disease. You will also precipitate DNA from an aqueous solution.
Background:
PCR is a widely used technique in molecular biology that enables amplification

(copying) of a desired DNA sequence. The process involves thermal cycling and
DNA synthesis from oligonucleotide primers (see Figure 6).
In thermal cycling there are three different temperatures per cycle - a denaturation
step which separates the DNA strands (usually 92 - 95°C); a step where the
oligonucleotide primers anneal to the DNA template (generally 50 - 65°C); and a step
at 72°C where the oligonucleotide primers are extended by Taq DNA polymerase.
These three temperatures constitute one cycle and usually 25 - 35 cycles are used in
each experiment.
The oligonucleotides provide the specificity for the reaction. They are usually
between 20 and 30 bases in length, which is sufficiently long to hybridise (base pair)
at only one sequence in the human genome. The oligonucleotides are synthesized
chemically in an automatic machine.
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Taq DNA polymerase is used because it is stable at high temperatures (92 - 95°C)
and its temperature optimum is 72°C. It was originally isolated from a bacteria
growing in thermal hot springs.
The PCR exponentially amplifies a DNA sequence. This is because in each cycle
the number of DNA strands doubles and hence over a million-fold amplification can
occur in 25 cycles. (See Figure 1 over page). In 1µg of human DNA (whose haploid
genome contains 3 X 109 bps of DNA), a unique sequence of 300 bp comprises
0.1 pg of DNA which is too small a quantity to be seen on an agarose gel (of course it
would be indistinguishable from the rest of the genome). If the 300 bp sequence can
be selectively amplified a million-fold by PCR, then the 0.1 µg can be visualized on
an agarose gel. This can be accomplished in an afternoon by the PCR technique.
DNA sequence:
The sequence that you will be attempting to amplify is an exon sequence from the
Duchenne’s Muscular Dystrophy (DMD) gene. Within this particular family pedigree,
there has been a deletion of approximately 200 bp within the coding sequence.
Following PCR amplification of the specific DNA sequence, deletions of this size can
be readily identified by agarose gel electrophoresis. Based on the experimental
results you should be able to complete a pedigree for this family and determine the
carriers and affected individuals and hence, the mode of transmission.
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Figure 6: Outline of PCR.

116
Procedure:
Within a demonstrator group, you want to analyze the DNA from every member of
the pedigree. Ensure that each student within your group has a different DNA
sample to analyze so that all the DNA samples are analyzed (there are a total of 15
DNA samples to be analyzed in this pedigree).
1. Pipette 20µl of DNA into a 0.2 ml PCR tube.
2. Add 4 µl of PCR mix.
This consists of (final concentration in 25 µl):

2 pmole forward oligonucleotide primer
2 pmole reverse oligonucleotide primer
200 µM dATP, 200 µM dCTP, 200 µM dTTP, 200 µM dGTP
16.6 mM (NH4)2SO4
67 mM Tris-HCl, pH 8.8 (at 25°C)
6.7 mM MgCl2
3. Add 1 µl of Taq DNA polymerase (supplied by your demonstrator).
4. Mix the contents of the tube by gently flicking the tube with your finger. Clearly
label the tube with your initials and give the tube to your demonstrator.
5. The tube will be placed in the PCR machine for thermal cycling and will be
returned to you at the next practical class.
6. Record here exactly what you did, including any mix-ups that might affect your
results: you will not be penalised for these, but the information is necessary to
interpret results properly next week.
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BABS Teaching Laboratory Practical 6: Genes II: Genetic

Inheritance
BABS_RA_BABS1201_8

demonstrators instructions
when handling all biological
demonstrator immediately of
any spills or other incidents.
Sharps Physical injury Use caution working with pipette
tips. Dispose of used tips in the
sharps bins on your bench.
Use of electrical equipment Electrocution, fire, tripping over Routine tagging and testing of
cables equipment, visual inspection
prior to use, do not use
damaged equipment until
repaired, don’t use near water
or flammables.
Chemicals (Taq DNA Do not get in on skin or clothing. Wear Personal protective
polymerase, Reaction buffer If you do, wash the affected equipment (gowns, gloves and
(10x), MgCl2, dNTP’s, forward area for several minutes with enclosed shoes). Wash hands
and reverse primers running water. before leaving the laboratory.
(oligonucleotides), template Wear gloves at all times.
DNA (or cDNA), milliQ water)
UV light (Gel doc UV damage to skin and/or eyes Ensure UV switches off when
transilluminator) door is opened. If not, switch off
equipment and immediately
notify staff.

appropriate liquid waste containers. Used pipette tips and microcentrifuge tubes should be placed
in approved biohazard sharps containers provided on your bench.

requirements.
Signature:……………………………………………………………Date:……………………………
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PRACTICAL 6
GENES II
GENETIC INHERITANCE
CONTENTS
1. Inheritance and Mendel’s laws

2. Investigating human pedigrees
3. Completion and analysis of PCR screening
4. Precipitation of genomic DNA from strawberries

Complete the following three Mastering Biology tutorial activity. This will also help
you prepare for your Mastering Biology Quiz 5, which is an assessable part of the
course.
ITEM MEDIAN
TITLE
TYPE TIME
Meiosis (3 of 3): Determinants of Heredity and Genetic
Tutorial 9 min
Variation (BioFlix tutorial)
OBJECTIVES
• Define and explain Mendel's law of segregation (the first law).

• Apply Mendel's first law to a simple cross between two heterozygous
individuals.
• Demonstrate the alternative possible arrangements of homologous chromosomes
during metaphase I of meiosis.
• Relate the arrangement of homologous chromosomes in metaphase I to the
number of types of genetically different gametes that can be produced.
• Define & explain Mendel's law of independent assortment (the second law).
• Verify that the law of independent assortment holds true for alleles in a dihybrid
cross between two heterozygous individuals.
results.
• Observe genomic DNA and its properties.
119
1. INHERITANCE AND MENDEL’S LAWS
Mendel’s first law: alleles segregate during meiosis (Drosophila genetics A)
Since there is a pair (the homologues) of each type of chromosome in a diploid

organism, there will also be a pair of each type of gene: one gene on one
chromosome and the second on its homologue. Genes for a particular trait are found
at the same locus (physical place or location) on each of the homologous
chromosomes. An allele is an alternative form of a gene. In some diploids, the two
homologous copies of a gene are identical and such organisms are said to be
homozygous. In contrast, in other organisms, the two copies are different; those
organisms with different alleles at a locus are said to be heterozygous. An
organism’s phenotype (its physical properties) depends in part on its genotype (the
allelic state of its genes).
During meiosis, homologous chromosomes are separated from each other, and only
one may be carried in a particular gamete or spore. Thus the gene copies carried on
each of the homologous chromosomes are also separated or segregated.
When a diploid is heterozygous, this segregation is significant because the haploid

gametes carry different alleles. Mendel's first law states that alleles segregate in
meiosis (Figure 1). When two haploid gametes combine during fertilization, two
alleles for each trait are again present in the offspring.
Figure 1: Alleles segregate during meiosis.
Why do the two chromatids of a chromosome have the same alleles (A and a) on one
dyad?
120
How are the A and a alleles distributed to the daughter cells?
Do your observations support Mendel's first law? Explain:
Using Drosophila to verify Mendel’s first law of segregation:
Mendel's first law can be verified by examining wing length in Drosophila

melanogaster bred from the union of gametes from two parents that differ in a
particular locus. In this example, there are two alleles, V and v. The phenotype of
the VV homozygote is full size wings, the phenotype of the vv homozygote is vestigial
or short wings, and the phenotype of the heterozygote (Vv) is full size wings.
Because the VV and Vv genotypes have the same phenotype, the allele V is
dominant, while v is recessive. By convention, the dominant allele is assigned the
capital letter. We can also say the full size wing phenotype is dominant to the
vestigial phenotype.
What size wings would the VV parent have?
What is the genotype of gametes produced by the VV parent?
What size wings would the vv parent have?
What is the genotype of gametes produced by the vv parent?
Consider the genotypes of gametes that can be produced by the homozygous

parents, VV and vv. What would be the genotype of all offspring resulting from the
union of one gamete from each parent?
121
What is the phenotype of the offspring in this generation (which is labeled F1)?
When F1 individuals make gametes, their alleles for wing size will segregate.What
are the genotypes of gametes produced by F1 individuals?
The consequences of this segregation of alleles will become apparent when one
examines the possible genotypes in the next generation (called F2 since it is
composed of the offspring produced by F1 individuals).
The possible combinations of alleles that may be produced in each parent's

gametes, and the results of these combinations in the genotypes of the offspring,
can be determined by using a table called a Punnett square. All of the possible
genotypes of gametes that can be produced by one parent are listed across the top
of the square; all genotypes of gametes that can be produced by the other parent
are listed along the side.
In the Punnett square below, one type of gamete from each F 1 parent has already
been listed, and one possible combination is shown. Fill in the blanks for the other
gamete genotype for each parent, and then complete the other three combinations
in the square to determine the possible genotypes of the offspring. (Note: By
convention, the dominant allele for each trait is written first: for example, Vv, not
vV.) Below the Punnett square, list the genotypes and phenotypes of the four
types of individuals produced in the F2 generation.
Gametes from father

Gametes from
V
mother
V VV (full)
Vv (full)
Genotype Phenotype___________
________ ____________________
________ ____________________
________ ____________________
________ ____________________
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How many different kinds of genotypes are present in the F2 generation?
Indicate below the expected proportion of individuals with these genotypes:
Homozygous Heterozygous Homozygous

dominant recessive
Genotype
Proportion
How many different kinds of phenotypes are present in the F2 generation?
In the table below, fill in the expected proportion of individuals showing these
phenotypes
Phenotype Proportion
Full wing
Short wing
Your demonstrator will supply you with a photograph simulation of randomly selected
F2 flies.
Record the total number of flies and then record number of flies with full size wings
and those with short wings.
Full wings Short wings

Your data
Class total
How do these numbers compare to the proportion you predicted?

123
Mendel’s second law: alleles of unlinked genes assort independently
Now let us consider meiosis involving two sets of homologous chromosomes. AlIeles
for trait A (A or a) are found on one pair of homologues. AlIeles for an entirely
different trait B (B or b) are found on the other pair of chromosomes. Assume that
two parents are each heterozygous for both genes. Each parent would have the
genotype AaBb.
It is possible for these parents to produce gametes AB and ab or aB and Ab,
depending on how the pairs of homologous chromosomes are arranged at
metaphase I of meiosis.
The alleles for the two genes sort themselves out independently. The behaviour of A
is not linked to that of B because the genes are on separate chromosomes (unlinked
genes). So, for example, the combination AB is as likely as the combination ab.
Mendel's second law states that alleles of unlinked genes assort independently
(Figure 2).
Figure 2: Allele combinations in haploid gametes or spores are produced by

independent assortment of alleles present on different chromosomes.
Since many gametes are produced at one time, a parent can produce gametes of all
four genotypes: Ab, ab, aB, and Ab. When considering the possible genotypes for
offspring, all gamete genotype possibilities for each parent must be considered.
Considering Mendel's second law, that alleles of unlinked genes assort

independently:
How many possible combinations of alleles exist if you consider the results from
both possibilities above?
124
How many different types of gametes can be made by an individual of genotype

AaBb?
Mendel’s second law can be verified by tracing the fate of two unlinked genes in
Drosophila through a series of crosses. In addition to the locus for wing length (with
alleles V and v) there is a locus that controls eye colour (with alleles S and s).
Homozygous recessives (ss) have white eyes, while the other two genotypes have
the dominant wild-type colour of red with a black glint in the centre. Suppose you
cross a VVss mother with a vvSS father. This is called a dihybrid cross.
Which alleles are present in the gametes of these parent types?
Find the possible genotypes that would be present in individuals of the F1 generation
by filling in the Punnett square below.
Gametes from
father
Gametes from
mother
What is the genotype of all individuals in the F1 generation?
What is the phenotype of all the individuals in the F1 generation?
Which alleles are present in gametes produced by F1 insects?

125
Use the Punnett square below to find the proportions of different genotypes in the F2
progeny resulting from all the possible unions of the various gametes produced by
the F1 generation.
Gametes from father
_______ _______ _______ _______
_______
Gametes from _______

mother
_______
_______
Circle all genotypes that result in a particular phenotype with the same wing size and
eye colour.
Indicate the expected proportions (ratios) of individuals showing the following

phenotypes:
full wing, red eye

full wing, white eye
short wing, red eye
short wing, white eye
126
Take another look at your flies (from the photograph simulation), particularly their
eyes. Observe the number of flies with red eyes and those with white eyes. Now
record the number of flies that have a) full wing + red eye, b) full wing + white eye, c)
short wing + red eye, and d) short wing + white eye, and add your data to the class
total.
Full wing + Full wing + Short wing + Short wing +

white eye red eye white eye red eye
Your data
Class total
Do your results support what you predicted from the Punnett square? Explain:
127
2. INVESTIGATING HUMAN PEDIGREES
Introduction
Once you have the data from your PCR experiment, you will use it to analyse a family
pedigree. A study of human genetics is complicated by the fact that, unlike other
species of animals or plants, our species is not bred experimentally and test crosses
cannot be made to order. One of the principal tools is the pedigree, a phenotypic
record of a family extending over several generations, showing whether each
individual is affected by some condition. We can use a standard format for such a
pedigree so that everyone can understand it. A standard set of symbols is used in
the pedigree shown in Figure 7.
marriage line
I unaffected unaffected
female male
offspring line
1 2 3 4
II
affected unaffected outsider affected
daughter daughter son
1 2
III
unaffected unaffected
grand-son grand-daughter
Figure 3: Example pedigree.
Each individual is identified by the generation, and the relative order of appearance
within that generation. Hence III 2 is the last individual shown in this pedigree.
Affected means that the individuals show some unusual condition, and symbols for
these individuals are shaded in the pedigree. Shading over only half of a symbol
indicates individuals who are known heterozygotes (carriers).
128
Analysing for a single-locus disorder such as Duchenne’s Muscular Dystrophy:
Single locus disorders can be inherited in a number of ways, depending on whether

they are dominant or recessive, or whether they are X-linked. Table 1 below shows a
list of possible modes of inheritance, and their outcomes. This assumes that the
abnormal alleles are very rare in the general population, which is true for most single
locus disorders.
What mode of inheritance is most likely for the disorder shown in Figure 7?
Table 1.
129
Investigation of colour vision deficiency:
If you consent, your demonstrators will test you for colour vision deficiency, a fairly
common genetic variant. Record the information below:
Table 2:
Male Female
Total number tested
Number with colour vision deficiency
Incidence of colour vision deficiency (% total

tested)
Proportion of total colour vision deficiency
individuals
Can you speculate as to the mode of transmission of colour vision deficiency?

Suggest how you might confirm this.
Investigation of common Mendelian variants in humans:
Many of us have common genetic variations that are harmless but help to make us
individual. Look at Table 3, and inspect as many members of the class as you can
for each trait. Record the numbers of each variant you find, together with the gender
of your subjects, and the frequency with which you find more than one variant in any
one person. Can you deduce any rules for inheritance of any of these?
130
Table 3.
Total Male Female
Widow’s peak
(a V-shaped hairline above the forehead)
Cleft chin
(a Y-shaped furrow on the chin)
Mid-digital hair
(hair on the middle joints of the fingers: may be
very fine)
Ear lobes
(the lobes of the ears can be free or attached:
record those attached)
Tongue rolling
(the ability to roll one’s tongue into a tube)
Darwin’s tubercle
(a small lump on the rim of the external ear)
Can you make any suggestions as to the mode of inheritance of any of these traits?
Explain:
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3. COMPLETION AND ANALYSIS OF PCR SCREENING
Following amplification of an exon from the DMD gene by PCR last week, you now
need to visualise the amplified DNA fragments. This is accomplished by separating the
DNA fragments using agarose gel electrophoresis and staining the samples to visualise
the DNA. You will prepare the gels, load your DNA, run the gels and visualise the DNA.
Background
Due to its repetitive structure, native double-stranded DNA has a constant charge per
unit length and, on average, a constant mass per unit length. DNA molecules,
because of their identical shape, will migrate in an electric field at a rate inversely
proportional to their length or mass. Consequently, one of the simplest and most
rapid means of separating DNA fragments of varying sizes is by electrophoresis in an
agarose gel using an alkaline buffer.
The DNA fragments are highly negatively charged and so migrate to the positive
electrode. Agarose is a complex mixture of polysaccharides isolated from seaweed.
When the agarose is heated in solution it will form a gel as it cools (like jelly). The
agarose provides a matrix where the pore size can be varied depending on the
percentage agarose in the gel. For example, a 0.7% gel will separate kilobase sized
fragments whereas a 1.5% gel can be used for fragments 100 –1000 base pairs
(these are very general estimates). The gels are usually produced as a horizontal
slab (approx. 4 mm thick) with GelRedTM used to detect the DNA. GelRedTM is a dye
molecule that binds to nucleic acids and produces a luminescence under ultraviolet
light. Very small amounts of DNA (less than 100 ng) can be detected by this method.
It is possible to estimate the size of DNA fragments by observing the distance of
migration relative to the migration of standard DNA molecules of known size.
Procedure:
Agarose gels will be prepared for you before the class.
You should perform the following steps. Each bench group should have two gels.
1. If not already done so, place the gel in the electrophoresis tank. Make sure that
the top of the gel (the end with the comb) is next to the negative electrode (black)
i.e. NOT at the end with the positive electrode.
2. Add enough running buffer to just cover the gel.
3. Carefully remove the comb from the gel and ensure that buffer enters the wells
that have been formed when the comb was removed. There should be no air
bubbles in the wells.
4. Add 5 µl of gel loading buffer (GLB) to your PCR sample.
5. Set the pipette to 6 µl and gently pipette the DNA/GLB mixture up and down to
ensure they are completely mixed.
6. Pipette 6 µl of this mix into the wells in the gel. Make sure you make a record of
which sample is loaded in which lane.
132
7. In the middle lane of the gel, load the molecular weight markers (labelled M).
8. When all the samples are loaded, place the lid on the electrophoresis apparatus
and attach the electrodes to the power supply using the leads provided. Make
sure that the top of the gel is attached to the negative electrode (black) so that the
negatively charged DNA will migrate through the gel to the positive electrode.
9. Run the gel (at 100 volts) until the bromophenol blue marker dye has migrated
half way.
10. While this is happening, perform the DNA precipitation (part 2 of this practical).
11. With the aid of your demonstrator, visualise the DNA in the gel using the Gel
Documentation system.
Analysis:
Estimate the size of the bands on the agarose gel, using the molecular weight
markers as a guide. The sizes of the marker bands are: 1000, 800, 600, 500, 400,
300, 200, 150, and 100 base pairs, with an additional faint band at 50 base pairs.
With this information, you should be able to determine which individuals in the
pedigree have a complete exon and which have a deletion. Use this to complete the
following pedigree.
I
1 2
II
1 2 3 4
III
1 2 3 4 5
IV
1 2 3 4
What is the mode of transmission of Duchenne’s Muscular Dystrophy?

133
4. PRECIPITATION OF GENOMIC DNA FROM STRAWBERRIES
Although DNA is packed so efficiently into cells that we cannot see it, it is possible to
isolate DNA from cells and precipitate the DNA from solution so that it is visible.
Indeed DNA can be isolated from almost any organism, including the food we eat
(provided it hasn’t been cooked).
DNA has been prepared for you from strawberries by using high salt solution and
detergent to lyse the cells, extract the nuclei, and release the DNA into solution.
You will precipitate the DNA from this aqueous solution by the addition of cold
alcohol.
1. Pipette approximately 1 ml of the aqueous DNA solution into a clean specimen

tube.
2. Using the 1 ml disposable plastic pipette, slowly add 2 ml of cold 95% ethanol.
Let the ethanol run down the side of the tube so that it forms a layer above the
aqueous DNA solution.
3. Using the pipette gently stir the layer where the ethanol touches the DNA solution.
You should observe the formation of long fibrous strands of DNA.
4. If you are careful, you should be able to pull the DNA out of the test tube by gently
swirling the pipette in the DNA layer and then pulling it through the alcohol layer
What colour is your DNA?
Pure DNA should be translucent. If it is whitish in colour then it still has some
proteins (called histones) attached to it.
Why does DNA appear stringy?
If you want to keep the DNA, gently ease it off the end of the pipette into a vial of
50% ethanol. Cap the vial tightly. In the PCR you used GelRedTM to visualise your
DNA under UV light.
What do you see? Are they the same or different?

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FACULTY OF SCIENCE

SCHOOL OF BIOTECHNOLOGY AND BIOMOLECULAR SCIENCES

Welcome to BABS1201 Molecules, Cells and Genes

The course consists of three interconnected learning components: a lecture series, a

We look forward to teaching you.

Rebecca and John

2. Check the BABS1201 Moodle site: https://moodle.telt.unsw.edu.au/login/index.php

3. Post your question to the forums in the BABS1201 Moodle site.

5. Take the time to clearly word your query.

• How do I find answers to questions about specific lecture material?

3. Use the Mastering Biology revision materials available via Moodle.

4. Post your question on a discussion forum in the BABS1201 Moodle site.

• How do I contact my demonstrator? Can I email them?

• Will I have access to past BABS1201 exam papers?

ABSENCES AND ASSESSMENTS

• I missed a lab class. What should I do?

• I missed the mid-session exam. What should I do?

• I could not submit my assessment on time. What should I do?

BABS1201 Weekly Class and Assessment Schedule – S1, 2018

Introduction to Introduction to Online lab safety

Course Name Molecules, Cells & Genes

Academic Unit School of Biotechnology and Biomolecular Sciences

Level of Course First Year Undergraduate

Administrative Support E-mail: BABS1201@unsw.edu.au

This textbook complements the Mastering biology learning resources available to

BABS1201 uses Moodle as an on-line course management software. This website

Course Assessment Schedule & Summary

A. Online This online laboratory safety quiz is accessable through the

Mastering Biology Assessment Schedule and Summary

UNSW Science Graduate Attributes Developed in this Course

Development of scientific writing skills through introduction

The laboratory program forms an essential element of the students’

o Teach students the process of scientific inquiry through progressive

Special Consideration and Further Assessment

• Originals or certified copies of your supporting documentation, and

The supporting documentation must be submitted to Student Central for

Further details are also available:

It is the responsibility of all students to regularly consult their official

In Session 1, the BABS1201 Supplementary Examination Period will be:

Saturday 14 July – Saturday 21 July

Academic Honesty and Plagiarism

Plagiarism is the presentation of the thoughts or work of another as one’s own.

Individual assistance is available on request from The Learning Centre.

Course Assessment – Detailed Instructions

A. Online Laboratory Safety Quiz – COMPULSORY

DUE: by 9am on the day of your first Practical Class

This quiz is compulsory, but does not comtribute to your grade.

B. Session Tests 1 and 2 – 10% each

The format of the exam is multiple choice questions.

C. Science Communication Project

1. Select a topic from the list provided;

8. Submit an individual REFLECTIVE SUMMARY (5%) that describes your personal

This project incorporates the following UNSW Science graduate attributes:

• Research, inquiry and analytical thinking abilities;

SUMMARY OF ASSESSABLE PROJECT COMPONENTS:

• Search for peer-reviewed scientific

• Effectively communicate ideas and Practical 4

• Effectively communicate ideas and

• Thoroughly and reliably record/document

• Maintain a diary of personal learning

Total Assessment Weighting: 35%

LIST OF PROJECT TOPICS:

18. Humans are still evolving and we can watch it happen